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Sample records for copia retrotransposon tos17

  1. Mobilized retrotransposon Tos17 of rice by alien DNA introgression transposes into genes and causes structural and methylation alterations of a flanking genomic region.

    PubMed

    Han, F P; Liu, Z L; Tan, M; Hao, S; Fedak, G; Liu, B

    2004-01-01

    Tos17 is a copia-like endogenous retrotransposon of rice, which can be activated by various stresses such as tissue culture and alien DNA introgression. To confirm element mobilization by introgression and to study possible structural and epigenetic effects of Tos17 insertion on its target sequences, we isolated all flanking regions of Tos17 in an introgressed rice line (Tong35) that contains minute amount of genomic DNA from wild rice (Zizania latifolia). It was found that there has been apparent but limited mobilization of Tos17 in this introgression line, as being reflected by increased but stable copy number of the element in progeny of the line. Three of the five activated copies of the element have transposed into genes. Based on sequence analysis and Southern blot hybridization with several double-enzyme digests, no structural change in Tos17 could be inferred in the introgression line. Cytosine methylation status at all seven CCGG sites within Tos17 was also identical between the introgression line and its rice parent (Matsumae)-all sites being heavily methylated. In contrast, changes in structure and cytosine methylation patterns were detected in one of the three low-copy genomic regions that flank newly transposed Tos17, and all changes are stably inherited through selfed generations. PMID:15703040

  2. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

    PubMed Central

    La, Honggui; Ding, Bo; Mishra, Gyan P.; Zhou, Bo; Yang, Hongmei; Bellizzi, Maria del Rosario; Chen, Songbiao; Meyers, Blake C.; Peng, Zhaohua; Zhu, Jian-Kang; Wang, Guo-Liang

    2011-01-01

    DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counteract transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli. PMID:21896764

  3. Target Site Specificity of the Tos17 Retrotransposon Shows a Preference for Insertion within Genes and against Insertion in Retrotransposon-Rich Regions of the Genome

    PubMed Central

    Miyao, Akio; Tanaka, Katsuyuki; Murata, Kazumasa; Sawaki, Hiromichi; Takeda, Shin; Abe, Kiyomi; Shinozuka, Yoriko; Onosato, Katsura; Hirochika, Hirohiko

    2003-01-01

    Because retrotransposons are the major component of plant genomes, analysis of the target site selection of retrotransposons is important for understanding the structure and evolution of plant genomes. Here, we examined the target site specificity of the rice retrotransposon Tos17, which can be activated by tissue culture. We have produced 47,196 Tos17-induced insertion mutants of rice. This mutant population carries ∼500,000 insertions. We analyzed >42,000 flanking sequences of newly transposed Tos17 copies from 4316 mutant lines. More than 20,000 unique loci were assigned on the rice genomic sequence. Analysis of these sequences showed that insertion events are three times more frequent in genic regions than in intergenic regions. Consistent with this result, Tos17 was shown to prefer gene-dense regions over centromeric heterochromatin regions. Analysis of insertion target sequences revealed a palindromic consensus sequence, ANGTT-TSD-AACNT, flanking the 5-bp target site duplication. Although insertion targets are distributed throughout the chromosomes, they tend to cluster, and 76% of the clusters are located in genic regions. The mechanisms of target site selection by Tos17, the utility of the mutant lines, and the knockout gene database are discussed. PMID:12897251

  4. Reverse genetics in rice using Tos17.

    PubMed

    Mieulet, Delphine; Diévart, Anne; Droc, Gaëtan; Lanau, Nadège; Guiderdoni, Emmanuel

    2013-01-01

    Transposon of Oryza sativa 17 (Tos17), a Ty1-Copia Class I retroelement, is one of the few active retroelements identified in rice, the main cereal crop of human consumption and the model genome for cereals. Tos17 exists in two copies in the standard Nipponbare japonica genome (n = 12 and 379 Mb). Tos17 copies are inactive in the plant grown under normal conditions. However, the copy located on chromosome 7 can be activated upon tissue culture. Plants regenerated from 3- and 5-month-old tissue cultures harbor, respectively, an average of 3.5 and 8 newly transposed copies that are stably inserted at new positions in the genome. Due to its favorable features, Tos17 has been extensively used for insertion mutagenesis of the model genome and 31,403 sequence indexed inserts harbored by regenerants/T-DNA plants are available in the databases. The corresponding seed stocks can be ordered from the laboratories which generated them. Both forward genetics and reverse genetics approaches using these lines have allowed the deciphering of gene function in rice. We report here two protocols for ascertaining the presence of a Tos17 insertion in a gene of interest among R2/T2 seeds received from Tos17 mutant stock centers: The first protocol is PCR-based and allows the identification of azygous, heterozygous and homozygous plants among progenies segregating the insertion. The second protocol is based on DNA blot analysis and can be used to identify homozygous plants carrying the Tos17 copy responsible for gene disruption while cleaning the mutant background from other unwitting mutagen inserts. PMID:23918431

  5. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.

    PubMed

    Dias, Elaine Silva; Hatt, Clémence; Hamon, Serge; Hamon, Perla; Rigoreau, Michel; Crouzillat, Dominique; Carareto, Claudia Marcia Aparecida; de Kochko, Alexandre; Guyot, Romain

    2015-09-01

    Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer. PMID:26245353

  6. Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants.

    PubMed Central

    Flavell, A J; Dunbar, E; Anderson, R; Pearce, S R; Hartley, R; Kumar, A

    1992-01-01

    We have used the polymerase chain reaction to isolate fragments of Ty1-copia group retrotransposons from a wide variety of members of the higher plant kingdom. 56 out of 57 species tested generate an amplified fragment of the size expected for reverse transcriptase fragments of Ty1-copia group retrotransposons. Sequence analysis of subclones shows that the PCR fragments display varying degrees of sequence heterogeneity. Sequence heterogeneity therefore seems a general property of Ty1-copia group retrotransposons of higher plants, in contrast to the limited diversity seen in retrotransposons of Saccharomyces cerevisiae and Drosophila melanogaster. Phylogenetic analysis of all these sequences shows, with some significant exceptions, that the degree of sequence divergence in the retrotransposon populations between any pair of species is proportional to the evolutionary distance between those species. This implies that sequence divergence during vertical transmission of Ty1-copia group retrotransposons within plant lineages has been a major factor in the evolution of Ty1-copia group retrotransposons in higher plants. Additionally, we suggest that horizontal transmission of this transposon group between different species has also played a role in this process. PMID:1379359

  7. Characterization and chromosomal organization of Ty1-copia retrotransposons in wax gourd.

    PubMed

    Jiang, Biao; Liu, Wenrui; Peng, Qingwu; He, Xiaoming; Xie, Dasen

    2014-11-01

    Wax gourd (2n=2x=24) is an important vegetable species in Cucurbitaceae. Because it can be stored for a very long period of time, it plays an important role in ensuring the annual supply and regulating off-season supply of the vegetables. However, the availability of genetic information about wax gourd is limited. This study aimed to identify the useful genetic information for wax gourd. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia retrotransposons were isolated from the genome of wax gourd using degenerate oligonucleotide primers. A total of twenty eight RT sequences were obtained, which showed high heterogeneity with the similarity ranging from 47.5% to 94.3%. Sixteen (57.1%) of them were found to be defective, being disrupted by stop codons and/or frameshift mutations. These 28 sequences were divided into five subfamilies. The comparative phylogenetic analysis with other Cucurbitaceae species from GenBank database showed that most retrotransposons derived from the same genus tended to cluster together, although there were a few exceptions. These results indicate that both vertical transmission and horizontal transmission are the sources of Ty1-copia retrotransposons in wax gourd. Fluorescent in situ hybridization (FISH) with Ty1-copia retrotransposon sequences as probes revealed that this kind of retrotransposons had a dispersed genomic organization, physically distributed among all the chromosomes of wax gourd, with clusters in the heterochromatin regions. This is the first report of Ty1-copia retrotransposons in wax gourd, which would be helpful for our understanding about the organization and evolutions of wax gourd genome and also provide valuable information for our utilization of wax gourd retrotransposons. PMID:25108132

  8. Copia-, Gypsy- and Line-like Retrotransposon Fragments in the Mitochondrial Genome of Arabidopsis Thaliana

    PubMed Central

    Knoop, V.; Unseld, M.; Marienfeld, J.; Brandt, P.; Sunkel, S.; Ullrich, H.; Brennicke, A.

    1996-01-01

    Several retrotransposon fragments are integrated in the mitochondrial genome of Arabidopsis thaliana. These insertions are derived from all three classes of nuclear retrotransposons, the Ty1/copia-, Ty3/gypsy- and non-LTR/LINE-families. Members of the Ty3/gypsy group of elements have not yet been identified in the nuclear genome of Arabidopsis. The varying degrees of similarity with nuclear elements and the dispersed locations of the sequences in the mitochondrial genome suggest numerous independent transfer-insertion events in the evolutionary history of this plant mitochondrial genome. Overall, we estimate remnants of retrotransposons to cover >/=5% of the mitochondrial genome in Arabidopsis. PMID:8852855

  9. Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species.

    PubMed

    Kuipers, A G; Heslop-Harrison, J S; Jacobsen, E

    1998-06-01

    The genus Alstroemeria contains species with large genomes (2C = 36.5-78.9 pg (17,600-38,000 Mb) in those species with 2n = 2x = 16). We investigated the diversity and genomic and chromosomal organisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Analysis of 33 PCR-amplified sequences corresponding to a conserved domain of the Ty1-copia reverse transcriptase (rt) gene showed high heterogeneity among predicted amino acid sequences; no two sequences were identical, but most fell into one of five subgroups. Levels of inter- and intra-specific heterogeneity of sequences were similar. HaeIII-digested genomic DNA of various Alstroemeria species contained distinct bands upon hybridisation with individual rt gene fragments. Hybridisation with the heterogeneous PCR pool of rt fragments (retrotransposon pool) revealed additional bands; some minor bands were characteristic of either Brazilian or Chilean species. In situ hybridisation of the retrotransposon pool from three species to metaphase chromosomes from the same species showed a dispersed distribution of the retrotransposon pool with exclusion from rDNA and other chromosomal sites. Alstroemeria pelegrina, which is without major heterochromatic sites, showed some clustering and small negative bands. The retrotransposon pool was excluded from major DAPI-staining bands in Alstroemeria aurea, but in contrast, the sites of the major tandemly repeated sequences in Alstroemeria inodora showed a hybridisation signal similar to that in the rest of the chromosomes. The data are discussed in the context of the contribution of Ty1-copia-like retrotransposons to plant genome size, their evolution, and their value for phylogenetic and biodiversity studies. PMID:9729770

  10. Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression.

    PubMed Central

    White, S E; Habera, L F; Wessler, S R

    1994-01-01

    The wx-K mutation results from the insertion of a copia-like retrotransposon into exon 12 of the maize waxy gene. This retrotransposon, named Hopscotch, has one long open reading frame encoding all of the domains required for transposition. Computer-assisted database searches using Hopscotch and other plant copia-like retroelements as query sequences have revealed that ancient, degenerate retrotransposon insertions are found in close proximity to 21 previously sequenced plant genes. The data suggest that these elements may be involved in gene duplication and the regulation of gene expression. Similar searches using the Drosophila retrotransposon copia did not reveal any retrotransposon-like sequences in the flanking regions of animal genes. These results, together with the recent finding that reverse-transcriptase sequences characteristic of copia-like elements are ubiquitous and diverse in plants, suggest that copia-like retrotransposons are an ancient component of plant genomes. Images PMID:7991537

  11. Isolation and characterization of novel Ty1-copia-like retrotransposons from lily.

    PubMed

    Lee, Sung-Il; Park, Kyong-Cheul; Son, Jae-Han; Hwang, Youn-Jung; Lim, Ki-Byung; Song, Ye-Su; Kim, Jong-Hwa; Kim, Nam-Soo

    2013-09-01

    Species of the genus Lilium are well known for their large genomes. Although expansion of noncoding repeated DNA is believed to account for this genome size, retroelement del Ty3-gypsy is the only one described so far in the genus Lilium. We isolated Ty1-copia elements from Lilium longiflorum and named them LIREs (lily retrotransposons). The long terminal repeats, primer binding site, and polypurine tract sequences are highly similar among the LIRE elements, indicating that they are in the same lineage. Although the protein-coding regions were highly decayed, the sequence motifs of the integrase, reverse transcriptase, and RNase H domains were identifiable as belonging to the order of Ty1-copia elements. Phylogenetic analysis and primer binding site sequences revealed that these elements belonged to the Ale lineage among the six lineages of plant Ty1-copia elements. Base substitutions in the long terminal repeats estimated that the integration times of the LIRE Ty1-copia elements were between 0.7 and 5.5 mya. In situ hybridization showed that the LIRE elements were present in all the chromosomes of L. longiflorum and L. lancifolium, but absent in centromeres, telomeres, and 45S rRNA sites in both species. The LIRE elements were present very abundantly in species of the genus Lilium, but absent in other genera of the family Liliaceae, implying that the LIRE elements might have contributed to the expansion of the genome in the genus Lilium. PMID:24168670

  12. pCal, a highly unusual Ty1/copia retrotransposon from the pathogenic yeast Candida albicans.

    PubMed Central

    Matthews, G D; Goodwin, T J; Butler, M I; Berryman, T A; Poulter, R T

    1997-01-01

    Retrotransposons are mobile genetic elements. They can transpose via the reverse transcription of mRNA into double-stranded DNA (dsDNA) followed by the insertion of this dsDNA into new sites within the host genome. The unintegrated, linear, dsDNA form of retrotransposons is usually very rare. We report here the isolation of a retrotransposon from Candida albicans which is unusual in this respect. This element, which we have named pCal, was first identified as a distinct band when uncut C. albicans DNA was examined on an agarose gel. Sequence analysis of the cloned element revealed that it is a retrotransposon belonging to the Ty1/copia group. It is estimated that pCal produces 50 to 100 free, linear, dsDNA copies of itself per cell. This is a much higher level of expression than even that of the system in which Ty1 is expressed behind the highly active GAL1 promoter on a high-copy-number plasmid (about 10 copies per cell). Another unusual feature of pCal is that its Pol enzymes are likely to be expressed via the pseudoknot-assisted suppression of an upstream, in-phase stop codon, as has been shown for Moloney murine leukemia virus. PMID:9371461

  13. Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups

    PubMed Central

    De Almeida, Luciane M; Carareto, Claudia MA

    2006-01-01

    Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5'LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. On the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families. PMID:16954045

  14. LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements

    PubMed Central

    Esnault, Caroline; Graça, Paula; Higuet, Dominique; Bonnivard, Eric

    2013-01-01

    Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a “domino days spreading” branching process in which successive amplifications may interact positively. PMID:23469217

  15. A LTR copia retrotransposon and Mutator transposons interrupt Pgip genes in cultivated and wild wheats.

    PubMed

    Di Giovanni, Michela; Cenci, Alberto; Janni, Michela; D'Ovidio, Renato

    2008-04-01

    Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. Wheat pgip genes have been isolated from the B (Tapgip1) and D (Tapgip2) genomes, and now we report the identification of pgip genes from the A genomes of wild and cultivated wheats. By Southern blots and sequence analysis of BAC clones we demonstrated that wheat contains a single copy pgip gene per genome and the one from the A genome, pgip3, is inactivated by the insertion of a long terminal repeat copia retrotranspon within the fourth LRR. We demonstrated also that this retrotransposon insertion is present in Triticum urartu and all the polyploidy wheats assayed, but is absent in T. monococcum (Tmpgip3), suggesting that this insertion took place after the divergence between T. monococcum and T. urartu, but before the formation of the polyploid wheats. We identified also two independent insertion events of new Class II transposable elements, Vacuna, belonging to the Mutator superfamily, that interrupted the Tdipgip1 gene of T. turgidum ssp. dicoccoides. The occurrence of these transposons within the coding region of Tdipgip1 facilitated the mapping of the Pgip locus in the pericentric region of the short arm of chromosome group 7. We speculate that the inactivation of pgip genes are tolerated because of redundancy of PGIP activities in the wheat genome. PMID:18301877

  16. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L.

    PubMed Central

    2013-01-01

    Background Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features of copia-type retrotransposons as ideal genetic tools for gene tagging, mutagenesis, and marker-assisted selection, they have not been characterized in the jatropha genome yet. Here, we examined the diversity, evolution, and genome-wide organization of copia-type retrotransposons in the Asian, African, and Mesoamerican accessions of jatropha, then introduced a retrotransposon-based marker for this biofuel crop. Results In total, 157 PCR fragments that were amplified using the degenerate primers for the reverse transcriptase (RT) domain of copia-type retroelements were sequenced and aligned to construct the neighbor-joining tree. Phylogenetic analysis demonstrated that isolated copia RT sequences were classified into ten families, which were then grouped into three lineages. An in-depth study of the jatropha genome for the RT sequences of each family led to the characterization of full consensus sequences of the jatropha copia-type families. Estimated copy numbers of target sequences were largely different among families, as was presence of genes within 5 kb flanking regions for each family. Five copia-type families were as appealing candidates for the development of DNA marker systems. A candidate marker from family Jc7 was particularly capable of detecting genetic variation among different jatropha accessions. Fluorescence in situ hybridization (FISH) to metaphase chromosomes reveals that copia-type retrotransposons are scattered across chromosomes mainly located in the distal part regions. Conclusion This is the first report on genome-wide analysis and the cytogenetic mapping of copia-type retrotransposons of jatropha, leading to the discovery of families bearing high potential as DNA

  17. Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements as major components of the genome.

    PubMed

    Schmidt, T; Kubis, S; Heslop-Harrison, J S

    1995-09-01

    DNA sequences of the reverse transcriptase gene of long terminal repeat (LTR) and non-LTR (non-viral) retrotransposons have been isolated and cloned from the genome of sugar beet (Beta vulgaris). Both retrotransposon types are highly amplified in sugar beet and may account for 2-5% of the genome. The BNR1 family, representing the first non-viral retrotransposon reported from a dicotyledonous species, shows homology to the mammalian L1 family of long interspersed repeated sequences (LINEs) and to retrotransposable elements from maize and lily. Sequences of the Tbv family are homologous to the Ty1-copia class of LTR retrotransposons. The BNR1 and Tbv retrotransposon families are characterized by sequence heterogeneity and are probably defective. The deduced peptide sequences were used to investigate the relation to other retroelements from plants, insects and mammals. Fluorescence in situ hybridization was used to investigate the physical distribution and revealed that both retrotransposon families are present on all sugar beet chromosomes and largely excluded from chromosomal regions harbouring the 18S-5.8S-25S rRNA genes. The BNR1 family is organized in discrete clusters, while the Tbv family of Ty1-copia-like retrotransposons shows a more uniform distribution along chromosome arms and is absent from some chromosomal regions. These contrasting distributions emphasize the differences in evolutionary amplification and dispersion mechanisms between the two types of retrotransposons. The in situ results of both elements reflect significant features of a higher order structure of the genome, as it is known for both short interspersed repeated sequences (SINEs) and LINEs in human. PMID:7551548

  18. Germline mutations induced by N-nitroso-N-ethylurea do not affect the inserted copia retrotransposon in a Drosophila melanogaster wa mutant.

    PubMed

    Baldrich, E; Velázquez, A; Xamena, N; Cabré, O

    2003-11-01

    The white-apricot (wa) mutant of Drosophila melanogaster is characterized by a copia retrotransposon inserted in the second intron of the white locus. After germinal exposure to the alkylating agent N-ethyl-N-nitrosourea, we have obtained new phenotypes in the offspring, mainly lighter eye colour, but not revertants to the original phenotype. Subsequent genetic crosses showed that only 3 out of 13 new mutant phenotypes were allelic. Three white gene regions were analysed by Southern blot in order to determine the nature of the mutations. These three regions were the 5' regulatory region, the copia insertion site and the 3' coding region. The results obtained indicate that the treatment does not induce the total or partial excision of copia in the white locus. Two of the new allelic mutants present a 5' or 3' deletion in the white locus. The other new phenotypes seem to be caused by mutations being induced in other loci acting as modifiers, most of them located on the X chromosome. PMID:14614188

  19. The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana.

    PubMed

    Matsunaga, Wataru; Kobayashi, Akie; Kato, Atsushi; Ito, Hidetaka

    2012-05-01

    Environmental stress influences genetic and epigenetic regulation in plant genomes. We previously reported that heat stress activated a copia-like retrotransposon named ONSEN. To investigate the heat sensitivity and transgenerational activation of ONSEN, we analyzed the stress response by temperature shift and multiple heat stress treatments. ONSEN was activated at 37°C, and the newly inserted ONSEN was transcriptionally active and mobile to the next generation subjected to heat stress, indicating that the regulation of ONSEN is independent of positional effects on the chromosome. Reciprocal crosses with activated ONSEN revealed that the transgenerational transposition was inherited from both sexes, indicating that the transposition is suppressed independently of gametophytic regulation. We showed previously that ONSEN was transposed in mutants deficient in small interfering RNA (siRNA) biogenesis, including nrpd2 and rdr2, but not dcl3. To define the functional redundancy of Dicer-like (DCL) proteins in Arabidopsis, we analyzed ONSEN activation in mutants deficient in DCL proteins, including dcl2, dcl3 and dcl4. ONSEN was nearly immobile in a single Dicer mutant; however, some transgenerational transpositions were observed in dcl2/dcl3/dcl4 triple mutants subjected to heat stress. This indicated that the Dicer family is redundant for ONSEN transposition. To examine the activation of ONSEN in undifferentiated cells, ONSEN transcripts and synthesized DNA were analyzed in heat-stressed callus tissue. In contrast to vegetative tissue, high accumulation of the transcripts and amplified DNA copies of ONSEN were detected in callus. This result indicated that ONSEN activation is controlled by cell-specific regulatory mechanisms. PMID:22173101

  20. Transpositional reactivation of two LTR retrotransposons in rice-Zizania recombinant inbred lines (RILs).

    PubMed

    Wang, Hong-Yan; Tian, Qin; Ma, Yi-Qiao; Wu, Ying; Miao, Gao-Jian; Ma, Yan; Cao, Dong-Hui; Wang, Xiao-Li; Lin, Chunjing; Pang, Jingsong; Liu, Bao

    2010-12-01

    Hybridization is prevalent in plants, which plays important roles in genome evolution. Apart from direct transfer and recombinatory generation of genetic variations by hybridization, de novo genetic instabilities can be induced by the process per se. One mechanism by which such de novo genetic variability can be generated by interspecific hybridization is transpositional reactivation of quiescent parental transposable elements (TEs) in the nascent hybrids. We have reported previously that introgressive hybridization between rice (Oryza sativa L.) and Zizania latifolia Griseb had induced rampant mobilization of three TEs, a copia-like LTR retrotransposon Tos17, a MITE mPing and a class II TE belonging to the hAT superfamily, Dart/nDart. In this study, we further found that two additional LTR retrotransposons, a gypsy-like (named RIRE2) and a copia-like (named Copia076), were also transpositionally reactivated in three recombinant inbred lines (RILs) derived from introgressive hybridization between rice and Z. latifolia. Novel bands of these two retroelements appeared in the RILs relative to their rice parental line (cv. Matsumae) in Southern blot, suggestive of retrotransposition, which was substantiated by transposon display (TD) and locus-specific PCR amplification for insertion sites. Both elements were found to be transcribed but at variable levels in the leaf tissue of the parental line and the RILs, suggesting that transcriptional control was probably not a mechanism for their transpositional activity in the RILs. Expression analysis of four genes adjacent to de novo insertions by Copia076 revealed marked difference in the transcript abundance for each of the genes between the RILs and their rice parental line, but the alterations in expression appeared unrelated with the retroelement insertions. PMID:21166796

  1. Identification and characterization of jute LTR retrotransposons:

    PubMed Central

    Ahmed, Salim; Shafiuddin, MD; Azam, Muhammad Shafiul; Islam, Md. Shahidul; Ghosh, Ajit

    2011-01-01

    Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome. PMID:22016842

  2. Identification and characterization of jute LTR retrotransposons:: Their abundance, heterogeneity and transcriptional activity.

    PubMed

    Ahmed, Salim; Shafiuddin, Md; Azam, Muhammad Shafiul; Islam, Md Shahidul; Ghosh, Ajit; Khan, Haseena

    2011-05-01

    Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome. PMID:22016842

  3. LTR Retrotransposons in Fungi

    PubMed Central

    Muszewska, Anna; Hoffman-Sommer, Marta; Grynberg, Marcin

    2011-01-01

    Transposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (<50 elements), others demonstrate huge expansions (>8000 elements). The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other. PMID:22242120

  4. Reverse transcriptase domain sequences from tree peony (Paeonia suffruticosa) long terminal repeat retrotransposons: sequence characterization and phylogenetic analysis

    PubMed Central

    Guo, Da-Long; Hou, Xiao-Gai; Jia, Tian

    2014-01-01

    Tree peony is an important horticultural plant worldwide of great ornamental and medicinal value. Long terminal repeat retrotransposons (LTR-retrotransposons) are the major components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their sequence characteristics, genetic distribution and transcriptional activity; however, no information about them is available in tree peony. Ty1-copia-like reverse transcriptase sequences were amplified from tree peony genomic DNA by polymerase chain reaction (PCR) with degenerate oligonucleotide primers corresponding to highly conserved domains of the Ty1-copia-like retrotransposons in this study. PCR fragments of roughly 270 bp were isolated and cloned, and 33 sequences were obtained. According to alignment and phylogenetic analysis, all sequences were divided into six families. The observed difference in the degree of nucleotide sequence similarity is an indication for high level of sequence heterogeneity among these clones. Most of these sequences have a frame shift, a stop codon, or both. Dot-blot analysis revealed distribution of these sequences in all the studied tree peony species. However, different hybridization signals were detected among them, which is in agreement with previous systematics studies. Reverse transcriptase PCR (RT-PCR) indicated that Ty1-copia retrotransposons in tree peony were transcriptionally inactive. The results provide basic genetic and evolutionary information of tree peony genome, and will provide valuable information for the further utilization of retrotransposons in tree peony. PMID:26019529

  5. A nest of LTR retrotransposons adjacent the disease resistance-priming gene NPR1 in Beta vulgaris L. U.S. Hybrid H20

    Technology Transfer Automated Retrieval System (TEKTRAN)

    LTR_STRUC and LTR FINDER analyses of a sugar beet BAC, with the NPR1 disease resistance priming gene, identified two distinct LTR (long terminal repeats) retrotransposons. BvRTR1 has two ORFs: one encoding a Ty1/copia-like integrase and the other a hypothetical gene. RTR1 is 10,833 bp in length inc...

  6. Retrotransposon activation followed by rapid repression in introgressed rice plants.

    PubMed

    Liu, B; Wendel, J F

    2000-10-01

    Plant retrotransposons are largely inactive during normal development, but may be activated by stresses. Both copia-like and gypsy-like retrotransposons of rice were activated by introgression of DNA from the wild species Zizania latifolia Griseb. The copy number increase was associated with cytosine methylation changes of the elements. Activity of the elements was ephemeral, as evidenced by nearly identical genomic Southern hybridization patterns among randomly chosen individuals both within and between generations for a given line, and the absence of transcripts based on Northern analysis. DNA hypermethylation, internal sequence deletion, and possibly other mechanisms are likely responsible for the rapid element repression. Implications of the retroelement dynamics on plant genome evolution are discussed. PMID:11081978

  7. Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

    PubMed Central

    Tetreault, Hannah M.; Ungerer, Mark C.

    2016-01-01

    The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny. PMID:27233667

  8. Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data.

    PubMed

    Tetreault, Hannah M; Ungerer, Mark C

    2016-01-01

    The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny. PMID:27233667

  9. LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

    PubMed Central

    Barghini, Elena; Natali, Lucia; Giordani, Tommaso; Cossu, Rosa Maria; Scalabrin, Simone; Cattonaro, Federica; Šimková, Hana; Vrána, Jan; Doležel, Jaroslav; Morgante, Michele; Cavallini, Andrea

    2015-01-01

    Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms. PMID:25428895

  10. Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges[W][OA

    PubMed Central

    Butelli, Eugenio; Licciardello, Concetta; Zhang, Yang; Liu, Jianjun; Mackay, Steve; Bailey, Paul; Reforgiato-Recupero, Giuseppe; Martin, Cathie

    2012-01-01

    Traditionally, Sicilian blood oranges (Citrus sinensis) have been associated with cardiovascular health, and consumption has been shown to prevent obesity in mice fed a high-fat diet. Despite increasing consumer interest in these health-promoting attributes, production of blood oranges remains unreliable due largely to a dependency on cold for full color formation. We show that Sicilian blood orange arose by insertion of a Copia-like retrotransposon adjacent to a gene encoding Ruby, a MYB transcriptional activator of anthocyanin production. The retrotransposon controls Ruby expression, and cold dependency reflects the induction of the retroelement by stress. A blood orange of Chinese origin results from an independent insertion of a similar retrotransposon, and color formation in its fruit is also cold dependent. Our results suggest that transposition and recombination of retroelements are likely important sources of variation in Citrus. PMID:22427337

  11. The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms.

    PubMed Central

    Kamm, A; Doudrick, R L; Heslop-Harrison, J S; Schmidt, T

    1996-01-01

    A DNA sequence, TPE1, representing the internal domain of a Ty1-copia retroelement, was isolated from genomic DNA of Pinus elliottii Engelm. var. elliottii (slash pine). Genomic Southern analysis showed that this sequence, carrying partial reverse transcriptase and integrase gene sequences, is highly amplified within the genome of slash pine and part of a dispersed element >4.8 kbp. Fluorescent in situ hybridization to metaphase chromosomes shows that the element is relatively uniformly dispersed over all 12 chromosome pairs and is highly abundant in the genome. It is largely excluded from centromeric regions and intercalary chromosomal sites representing the 18S-5.8S-25S rRNA genes. Southern hybridization with specific DNA probes for the reverse transcriptase gene shows that TPE1 represents a large subgroup of heterogeneous Ty1-copia retrotransposons in Pinus species. Because no TPE1 transcription could be detected, it is most likely an inactive element--at least in needle tissue. Further evidence for inactivity was found in recombinant reverse transcriptase and integrase sequences. The distribution of TPE1 within different gymnosperms that contain Ty1-copia group retrotransposons, as shown by a PCR assay, was investigated by Southern hybridization. The TPE1 family is highly amplified and conserved in all Pinus species analyzed, showing a similar genomic organization in the three- and five-needle pine species investigated. It is also present in spruce, bald cypress (swamp cypress), and in gingko but in fewer copies and a different genomic organization. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8610105

  12. Restricting retrotransposons: a review.

    PubMed

    Goodier, John L

    2016-01-01

    Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research. PMID:27525044

  13. Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus

    PubMed Central

    Harkess, Alex; Mercati, Francesco; Abbate, Loredana; McKain, Michael; Pires, J. Chris; Sala, Tea; Sunseri, Francesco; Falavigna, Agostino; Leebens-Mack, Jim

    2016-01-01

    Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once, or possibly twice, in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n = 2× = 20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here, we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion, or to retrotransposon proliferation in dioecious species. We first estimate genome sizes, or use published values, for four hermaphrodites and four dioecious species distributed across the phylogeny, and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach, we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication (WGD) event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing, and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements, in particular, have undergone a marked proliferation in dioecious species. In the absence of a detectable WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species. PMID:27342737

  14. Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

    PubMed

    Harkess, Alex; Mercati, Francesco; Abbate, Loredana; McKain, Michael; Pires, J Chris; Sala, Tea; Sunseri, Francesco; Falavigna, Agostino; Leebens-Mack, Jim

    2016-01-01

    Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once, or possibly twice, in the genus Asparagus Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n = 2× = 20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here, we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion, or to retrotransposon proliferation in dioecious species. We first estimate genome sizes, or use published values, for four hermaphrodites and four dioecious species distributed across the phylogeny, and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach, we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication (WGD) event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing, and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements, in particular, have undergone a marked proliferation in dioecious species. In the absence of a detectable WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species. PMID:27342737

  15. Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza

    PubMed Central

    Hsu, Yu-Chia; Wang, Chang-Sheng; Lin, Yann-Rong; Wu, Yong-Pei

    2016-01-01

    Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5–5.0 Mya. A total of 37 different orthologous insertions of RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93–11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, RTPOSON, might have an impact on genome evolution, genic innovation, and genetic variation. PMID:26819544

  16. Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster.

    PubMed Central

    Kim, A; Terzian, C; Santamaria, P; Pélisson, A; Purd'homme, N; Bucheton, A

    1994-01-01

    Retroviruses are commonly considered to be restricted to vertebrates. However, the genome of many eukaryotes contains mobile sequences known as retrotransposons with long terminal repeats (LTR retrotransposons) or viral retrotransposons, showing similarities with integrated proviruses of retroviruses, such as Ty elements in Saccharomyces cerevisiae, copia-like elements in Drosophila, and endogenous proviruses in vertebrates. The gypsy element of Drosophila melanogaster has LTRs and contains three open reading frames, one of which encodes potential products similar to gag-specific protease, reverse transcriptase, and endonuclease. It is more similar to typical retroviruses than to LTR retrotransposons. We report here experiments showing that gypsy can be transmitted by microinjecting egg plasma from embryos of a strain containing actively transposing gypsy elements into embryos of a strain originally devoid of transposing elements. Horizontal transfer is also observed when individuals of the "empty" stock are raised on medium containing ground pupae of the stock possessing transposing elements. These results suggest that gypsy is an infectious retrovirus and provide evidence that retroviruses also occur in invertebrates. Images PMID:8108403

  17. Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza.

    PubMed

    Hsu, Yu-Chia; Wang, Chang-Sheng; Lin, Yann-Rong; Wu, Yong-Pei

    2016-01-01

    Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5-5.0 Mya. A total of 37 different orthologous insertions of RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93-11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, RTPOSON, might have an impact on genome evolution, genic innovation, and genetic variation. PMID:26819544

  18. Characterization of the LTR retrotransposon repertoire of a plant clade of six diploid and one tetraploid species.

    PubMed

    Piednoël, Mathieu; Carrete-Vega, Greta; Renner, Susanne S

    2013-08-01

    Comparisons of closely related species are needed to understand the fine-scale dynamics of retrotransposon evolution in flowering plants. Towards this goal, we classified the long terminal repeat (LTR) retrotransposons from six diploid and one tetraploid species of Orobanchaceae. The study species are the autotrophic, non-parasitic Lindenbergia philippensis (as an out-group) and six closely related holoparasitic species of Orobanche [O. crenata, O. cumana, O. gracilis (tetraploid) and O. pancicii] and Phelipanche (P. lavandulacea and P. ramosa). All major plant LTR retrotransposon clades could be identified, and appear to be inherited from a common ancestor. Species of Orobanche, but not Phelipanche, are enriched in Ty3/Gypsy retrotransposons due to a diversification of elements, especially chromoviruses. This is particularly striking in O. gracilis, where tetraploidization seems to have contributed to the Ty3/Gypsy enrichment and led to the emergence of seven large species-specific families of chromoviruses. The preferential insertion of chromoviruses in heterochromatin via their chromodomains might have favored their diversification and enrichment. Our phylogenetic analyses of LTR retrotransposons from Orobanchaceae also revealed that the Bianca clade of Ty1/Copia and the SMART-related elements are much more widely distributed among angiosperms than previously known. PMID:23663083

  19. Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats.

    PubMed

    Konovalov, Fedor A; Goncharov, Nikolay P; Goryunova, Svetlana; Shaturova, Aleksandra; Proshlyakova, Tatyana; Kudryavtsev, Alexander

    2010-06-01

    Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive. PMID:20407790

  20. Isolation and characterization of recombinant Drosophila Copia aspartic proteinase.

    PubMed

    Athauda, Senarath B P; Yoshioka, Katsuji; Shiba, Tadayoshi; Takahashi, Kenji

    2006-11-01

    The wild type Copia Gag precursor protein of Drosophila melanogaster expressed in Escherichia coli was shown to be processed autocatalytically to generate two daughter proteins with molecular masses of 33 and 23 kDa on SDS/PAGE. The active-site motif of aspartic proteinases, Asp-Ser-Gly, was present in the 23 kDa protein corresponding to the C-terminal half of the precursor protein. The coding region of this daughter protein (152 residues) in the copia gag gene was expressed in E. coli to produce the recombinant enzyme protein as inclusion bodies, which was then purified and refolded to create the active enzyme. Using the peptide substrate His-Gly-Ile-Ala-Phe-Met-Val-Lys-Glu-Val-Asn (cleavage site: Phe-Met) designed on the basis of the sequence of the cleavage-site region of the precursor protein, the enzymatic properties of the proteinase were investigated. The optimum pH and temperature of the proteinase toward the synthetic peptide were 4.0 and 70 degrees C respectively. The proteolytic activity was increased with increasing NaCl concentration in the reaction mixture, the optimum concentration being 2 M. Pepstatin A strongly inhibited the enzyme, with a Ki value of 15 nM at pH 4.0. On the other hand, the active-site residue mutant, in which the putative catalytic aspartic acid residue was mutated to an alanine residue, had no activity. These results show that the Copia proteinase belongs to the family of aspartic proteinases including HIV proteinase. The B-chain of oxidized bovine insulin was hydrolysed at the Leu15-Tyr16 bond fairly selectively. Thus the recombinant Copia proteinase partially resembles HIV proteinase, but is significantly different from it in certain aspects. PMID:16813567

  1. Isolation and chromosomal distribution of a novel Ty1-copia-like sequence from Secale, which enables identification of wheat-Secale africanum introgression lines.

    PubMed

    Jia, J; Yang, Z; Li, G; Liu, Ch; Lei, M; Zhang, T; Zhou, J; Ren, Z

    2009-01-01

    A repetitive sequence of 411 bp, named pSaO5411, was identified in the Secale africanum genome (Ra) by random amplified polymorphic DNA (RAPD) analysis of wheat and wheat-S. africanum amphiploids. GenBank BLAST search revealed that the sequence of pSaO5411 was highly homologous to a part of a Ty1-copia retrotransposon. Fluorescence in situ hybridization (FISH) analyses indicated that pSaO5411 was significantly hybridized to S. africanum chromosomes of a wheat-S. africanum amphiploid, and it was dispersed along the Secale chromosome arms except the terminal regions. Basing on the sequence of pSaO5411, a pair of sequence-characterized amplified region (SCAR) primers were designed, and the resultant SCAR marker was able to target both cultivated rye and the wild Secale species, which also enabled to identify effectively the S. africanum chromatin introduced into the wheat genome. PMID:19193979

  2. Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements

    PubMed Central

    Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; de Kochko, Alexandre; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

    2015-01-01

    A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes. PMID:25573958

  3. LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers.

    PubMed

    Tam, Sheh May; Lefebvre, Véronique; Palloix, Alain; Sage-Palloix, Anne-Marie; Mhiri, Corinne; Grandbastien, Marie-Angèle

    2009-10-01

    Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution. PMID:19618162

  4. LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice

    PubMed Central

    Wang, Hao; Liu, Jin-Song

    2008-01-01

    Background Long terminal repeat retrotransposons (LTR elements) are ubiquitous Eukaryotic TEs that transpose through RNA intermediates. Accounting for significant proportion of many plant genomes, LTR elements have been well established as one of the major forces underlying the evolution of plant genome size, structure and function. The accessibility of more than 40% of genomic sequences of the model legume Medicago truncatula (Mt) has made the comprehensive study of its LTR elements possible. Results We use a newly developed tool LTR_FINDER to identify LTR retrotransposons in the Mt genome and detect 526 full-length elements as well as a great number of copies related to them. These elements constitute about 9.6% of currently available genomic sequences. They are classified into 85 families of which 64 are reported for the first time. The majority of the LTR retrotransposons belong to either Copia or Gypsy superfamily and the others are categorized as TRIMs or LARDs by their length. We find that the copy-number of Copia-like families is 3 times more than that of Gypsy-like ones but the latter contribute more to the genome. The analysis of PBS and protein-coding domain structure of the LTR families reveals that they tend to use only 4–5 types of tRNAs and many families have quite conservative ORFs besides known TE domains. For several important families, we describe in detail their abundance, conservation, insertion time and structure. We investigate the amplification-deletion pattern of the elements and find that the detectable full-length elements are relatively young and most of them were inserted within the last 0.52 MY. We also estimate that more than ten million bp of the Mt genomic sequences have been removed by the deletion of LTR elements and the removal of the full-length structures in Mt has been more rapid than in rice. Conclusion This report is the first comprehensive description and analysis of LTR retrotransposons in the Mt genome. Many important

  5. How retrotransposons shape genome regulation.

    PubMed

    Mita, Paolo; Boeke, Jef D

    2016-04-01

    Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease. PMID:26855260

  6. The Ty1 Retrotransposon Restriction Factor p22 Targets Gag

    PubMed Central

    Tucker, Jessica M.; Larango, Morgan E.; Wachsmuth, Lucas P.; Kannan, Natarajan; Garfinkel, David J.

    2015-01-01

    A novel form of copy number control (CNC) helps maintain a low number of Ty1 retrovirus-like transposons in the Saccharomyces genome. Ty1 produces an alternative transcript that encodes p22, a trans-dominant negative inhibitor of Ty1 retrotransposition whose sequence is identical to the C-terminal half of Gag. The level of p22 increases with copy number and inhibits normal Ty1 virus-like particle (VLP) assembly and maturation through interactions with full length Gag. A forward genetic screen for CNC-resistant (CNCR) mutations in Ty1 identified missense mutations in GAG that restore retrotransposition in the presence of p22. Some of these mutations map within a predicted UBN2 domain found throughout the Ty1/copia family of long terminal repeat retrotransposons, and others cluster within a central region of Gag that is referred to as the CNCR domain. We generated multiple alignments of yeast Ty1-like Gag proteins and found that some Gag proteins, including those of the related Ty2 elements, contain non-Ty1 residues at multiple CNCR sites. Interestingly, the Ty2-917 element is resistant to p22 and does not undergo a Ty1-like form of CNC. Substitutions conferring CNCR map within predicted helices in Ty1 Gag that overlap with conserved sequence in Ty1/copia, suggesting that p22 disturbs a central function of the capsid during VLP assembly. When hydrophobic residues within predicted helices in Gag are mutated, Gag level remains unaffected in most cases yet VLP assembly and maturation is abnormal. Gag CNCR mutations do not alter binding to p22 as determined by co-immunoprecipitation analyses, but instead, exclude p22 from Ty1 VLPs. These findings suggest that the CNCR alleles enhance retrotransposition in the presence of p22 by allowing productive Gag-Gag interactions during VLP assembly. Our work also expands the strategies used by retroviruses for developing resistance to Gag-like restriction factors to now include retrotransposons. PMID:26451601

  7. Tyrosine Recombinase Retrotransposons and Transposons.

    PubMed

    Poulter, Russell T M; Butler, Margi I

    2015-04-01

    Retrotransposons carrying tyrosine recombinases (YR) are widespread in eukaryotes. The first described tyrosine recombinase mobile element, DIRS1, is a retroelement from the slime mold Dictyostelium discoideum. The YR elements are bordered by terminal repeats related to their replication via free circular dsDNA intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. Recently a large number of YR retrotransposons have been described, including elements from fungi (mucorales and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish, amphibia and reptiles. YR retrotransposons can be divided into three major groups: the DIRS elements, PAT-like and the Ngaro elements. The three groups form distinct clades on phylogenetic trees based on alignments of reverse transcriptase/ribonuclease H (RT/RH) and YR sequences, and also having some structural distinctions. A group of eukaryote DNA transposons, cryptons, also carry tyrosine recombinases. These DNA transposons do not encode a reverse transcriptase. They have been detected in several pathogenic fungi and oomycetes. Sequence comparisons suggest that the crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon. This acquisition must have occurred at a very early point in the evolution of eukaryotes. PMID:26104693

  8. The RNA interference proteins and vasa locus are involved in the silencing of retrotransposons in the female germline of Drosophila melanogaster.

    PubMed

    Vagin, Vasily V; Klenov, Mikhail S; Kalmykova, Alla I; Stolyarenko, Anastasia D; Kotelnikov, Roman N; Gvozdev, Vladimir A

    2004-05-01

    RNA interference (RNAi) is considered as a defense against expansion of transposable elements. The proteins related to RNA helicase and Argonaute families are involved in RNAi process in different organisms. It was shown that Argonaute AUBERGINE and putative RNA helicase SPINDLE-E proteins were essential for RNAi in Drosophila. Here, we describe the role of aubergine (aub) and spindle-E (spn-E) genes in the control of LTR retrotransposon copia and nonLTR telomeric Het-A and I retrotransposons in ovaries. spn-E mutation causes a drastically increased lacZ expression driven by copia LTR. For the first time we show the involvement of AUBERGINE protein and VASA RNA helicase, essential for oocyte patterning, in the retrotransposon silencing. spn-E, vasa and aub mutations cause similar accumulation of both I element and Het-A transcripts in the developing oocyte. VASA and AUBERGINE proteins are known as components of perinuclear ribonucleoprotein particles in germ cells, and spn-E mutation disturbs protein content of the particles. We suggest participation of these proteins in the same silencing pathway. PMID:17194939

  9. Evidence for the recent horizontal transfer of long terminal repeat retrotransposon

    PubMed Central

    Jordan, I. King; Matyunina, Lilya V.; McDonald, John F.

    1999-01-01

    The evolutionary dynamics existing between transposable elements (TEs) and their host genomes have been likened to an “arms race.” The selfish drive of TEs to replicate, in turn, elicits the evolution of host-mediated regulatory mechanisms aimed at repressing transpositional activity. It has been postulated that horizontal (cross-species) transfer may be one effective strategy by which TEs and other selfish genes can escape host-mediated silencing mechanisms over evolutionary time; however, to date, the most definitive evidence that TEs horizontally transfer between species has been limited to class II or DNA-type elements. Evidence that the more numerous and widely distributed retroelements may also be horizontally transferred between species has been more ambiguous. In this paper, we report definitive evidence for a recent horizontal transfer of the copia long terminal repeat retrotransposon between Drosophila melanogaster and Drosophila willistoni. PMID:10535972

  10. A dosage-sensitive modifier of retrotransposon-induced alleles of the Drosophila white locus.

    PubMed Central

    Rabinow, L; Birchler, J A

    1989-01-01

    The apricot allele of the white locus results from the insertion of the retrotransposon copia. Mutations in a newly discovered locus, the Darkener-of-apricot (Doa), suppress wa and some of its revertants. Of 44 other white alleles tested, only wsp55 is affected by Doa, although, in contrast, it is enhanced by Doa mutations. The Doa locus modulates wa and wsp55 expression as a function of its own dosage. Mutations in Doa are dominant suppressors or enhancers and are recessive lethals. Rare Doa mutant homozygotes escaping lethality demonstrate extreme phenotypic suppression of wa and enhancement of wsp55. RNA from wa is substantially wild-type in structure in escapers, although reduced in quantity. Images PMID:2542025

  11. The 5' termini of RNAs encoded by the transposable element copia.

    PubMed Central

    Flavell, A J; Levis, R; Simon, M A; Rubin, G M

    1981-01-01

    The 5' termini of copia-specific RNAs in Drosophila melanogaster tissue culture cells were determined by S1 nuclease mapping and cap analysis. Both major copia RNAs share an identical set of heterogeneous 5' ends. Three major cap 1 structures M7GpppCmpUp, M7GpppCmpCp and M7GpppGmpUp together with several other minor caps were found. Almost all the 5' termini, as judged by S-1 nuclease mapping, were located either in a pyrimidine-rich part of the terminal direct repeat or apparently outside of the copia element, suggesting that a proportion of copia transcripts derive from promoters external to the genetic element. Images PMID:6275356

  12. DIRS and Ngaro Retrotransposons in Fungi

    PubMed Central

    Muszewska, Anna; Steczkiewicz, Kamil; Ginalski, Krzysztof

    2013-01-01

    Retrotransposons with a tyrosine recombinase (YR) have been discovered recently and lack thorough annotation in fungi. YR retrotransposons are divided into 3 groups: DIRS, Ngaro and VIPER (known only from kinetoplastida). We used comparative genomics to investigate the evolutionary patterns of retrotransposons in the fungal kingdom. The identification of both functional and remnant elements provides a unique view on both recent and past transposition activity. Our searches covering a wide range of fungal genomes allowed us to identify 2241 YR retrotransposons. Based on CLANS clustering of concatenated sequences of the reverse transcriptase (RT), RNase H (RH), DNA N-6-adenine-methyltransferase (MT) and YR protein domains we propose a revised classification of YR elements expanded by two new categories of Ngaro elements. A phylogenetic analysis of 477 representatives supports this observation and additionally demonstrates that DIRS and Ngaro abundance changed independently in Basidiomycota and Blastocladiomycota/Mucoromycotina/Kixellomycotina. Interestingly, a single remnant Ngaro element could be identified in an Ascomycota genome. Our analysis revealed also that 3 Pucciniomycotina taxa, known for their overall mobile element abundance and big genome size, encode an elevated number of Ngaro retrotransposons. Considering the presence of DIRS elements in all analyzed Mucoromycotina, Kickxellomycotina and Blastocladiomycota genomes one might assume a common origin of fungal DIRS retrotransposons with a loss in Dicarya. Ngaro elements described to date from Opisthokonta, seem to have invaded the common ancestor of Agaricomycotina and Pucciniomycotina after Ustilagomycotina divergence. Yet, most of analyzed genomes are devoid of YR elements and most identified retrotransposons are incomplete. PMID:24086727

  13. DIRS and Ngaro Retrotransposons in Fungi.

    PubMed

    Muszewska, Anna; Steczkiewicz, Kamil; Ginalski, Krzysztof

    2013-01-01

    Retrotransposons with a tyrosine recombinase (YR) have been discovered recently and lack thorough annotation in fungi. YR retrotransposons are divided into 3 groups: DIRS, Ngaro and VIPER (known only from kinetoplastida). We used comparative genomics to investigate the evolutionary patterns of retrotransposons in the fungal kingdom. The identification of both functional and remnant elements provides a unique view on both recent and past transposition activity. Our searches covering a wide range of fungal genomes allowed us to identify 2241 YR retrotransposons. Based on CLANS clustering of concatenated sequences of the reverse transcriptase (RT), RNase H (RH), DNA N-6-adenine-methyltransferase (MT) and YR protein domains we propose a revised classification of YR elements expanded by two new categories of Ngaro elements. A phylogenetic analysis of 477 representatives supports this observation and additionally demonstrates that DIRS and Ngaro abundance changed independently in Basidiomycota and Blastocladiomycota/Mucoromycotina/Kixellomycotina. Interestingly, a single remnant Ngaro element could be identified in an Ascomycota genome. Our analysis revealed also that 3 Pucciniomycotina taxa, known for their overall mobile element abundance and big genome size, encode an elevated number of Ngaro retrotransposons. Considering the presence of DIRS elements in all analyzed Mucoromycotina, Kickxellomycotina and Blastocladiomycota genomes one might assume a common origin of fungal DIRS retrotransposons with a loss in Dicarya. Ngaro elements described to date from Opisthokonta, seem to have invaded the common ancestor of Agaricomycotina and Pucciniomycotina after Ustilagomycotina divergence. Yet, most of analyzed genomes are devoid of YR elements and most identified retrotransposons are incomplete. PMID:24086727

  14. Retrotransposon evolution in diverse plant genomes.

    PubMed Central

    Langdon, T; Seago, C; Mende, M; Leggett, M; Thomas, H; Forster, J W; Jones, R N; Jenkins, G

    2000-01-01

    Retrotransposon or retrotransposon-like sequences have been reported to be conserved components of cereal centromeres. Here we show that the published sequences are derived from a single conventional Ty3-gypsy family or a nonautonomous derivative. Both autonomous and nonautonomous elements are likely to have colonized Poaceae centromeres at the time of a common ancestor but have been maintained since by active retrotransposition. The retrotransposon family is also present at a lower copy number in the Arabidopsis genome, where it shows less pronounced localization. The history of the family in the two types of genome provides an interesting contrast between "boom and bust" and persistent evolutionary patterns. PMID:10978295

  15. Activation of tobacco retrotransposons during tissue culture.

    PubMed Central

    Hirochika, H

    1993-01-01

    Sequences of at least three new families of retrotransposons (Tto1-Tto3) were amplified by PCR from cDNA prepared from protoplasts of an established tobacco cell line, based on the fact that certain amino acids are highly conserved in the reverse transcriptases encoded by retrotransposons. Structural analysis indicates that Tto1 is 5.5 kb long and has features typical of retrotransposons. Transcription of Tto1 starting in the long terminal repeat was active only in cultured cells. Protoplast formation enhanced the transcription. The copy number of Tto1 increased 10-fold in established cell lines; it also increased in plants regenerated from tissue cultures and in transgenic plants. These results indicate that Tto1 is activated during tissue culture. This is the first demonstration of activation of a plant retrotransposon by tissue culture. The copy number of Tto2 and a previously isolated transposon, Tnt1, also increased in established cell lines, indicating that these two retrotransposons may also be activated by tissue culture. These three retrotransposons are cryptic in normally propagated plants: no difference in the copy number was observed between individuals of the same cultivars or even between different cultivars. Images PMID:8389699

  16. Eukaryote DIRS1-like retrotransposons: an overview

    PubMed Central

    2011-01-01

    Background DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and little is known about their origin and dynamics. Recently, we have shown that these retrotransposons are common among decapods, which calls into question the distribution of DIRS1-like retrotransposons among eukaryotes. Results To determine the distribution of DIRS1-like retrotransposons, we developed a new computational tool, ReDoSt, which allows us to identify well-conserved DIRS1-like elements. By screening 274 completely sequenced genomes, we identified more than 4000 DIRS1-like copies distributed among 30 diverse species which can be clustered into roughly 300 families. While the diversity in most species appears restricted to a low copy number, a few bursts of transposition are strongly suggested in certain species, such as Danio rerio and Saccoglossus kowalevskii. Conclusion In this study, we report 14 new species and 8 new higher taxa that were not previously known to harbor DIRS1-like retrotransposons. Now reported in 61 species, these elements appear widely distributed among eukaryotes, even if they remain undetected in streptophytes and mammals. Especially in unikonts, a broad range of taxa from Cnidaria to Sauropsida harbors such elements. Both the distribution and the similarities between the DIRS1-like element phylogeny and conventional phylogenies of the host species suggest that DIRS1-like retrotransposons emerged early during the radiation of eukaryotes. PMID:22185659

  17. What might retrotransposons teach us about aging?

    PubMed

    Maxwell, Patrick H

    2016-05-01

    Retrotransposons are activated as organisms age, based on work from several model systems. Since these mobile DNA elements can promote genome instability, this has raised the possibility that they can contribute to loss of cellular function with age. Many questions remain to be addressed about the relationship between retrotransposons and aging, so it is unclear if changes in their activity will be found to contribute to aging or to be a consequence of aging. A few broad perspectives are presented regarding how continued work on these elements could provide important insights into the aging process, regardless of whether their mobility is ultimately found to significantly contribute to reduced lifespan and healthspan. PMID:26581630

  18. Skipper, an LTR retrotransposon of Dictyostelium.

    PubMed Central

    Leng, P; Klatte, D H; Schumann, G; Boeke, J D; Steck, T L

    1998-01-01

    The complete sequence of a retrotransposon from Dictyostelium discoideum , named skipper , was obtained from cDNA and genomic clones. The sequence of a nearly full-length skipper cDNA was similar to that of three other partially sequenced cDNAs. The corresponding retrotransposon is represented in approximately 15-20 copies and is abundantly transcribed. Skipper contains three open reading frames (ORFs) with an unusual sequence organization, aspects of which resemble certain mammalian retroviruses. ORFs 1 and 3 correspond to gag and pol genes; the second ORF, pro, corresponding to protease, was separated from gag by a single stop codon followed shortly thereafter by a potential pseudoknot. ORF3 (pol) was separated from pro by a +1 frameshift. ORFs 2 and 3 overlapped by 32 bp. The computed amino acid sequences of the skipper ORFs contain regions resembling retrotransposon polyprotein domains, including a nucleic acid binding protein, aspartyl protease, reverse transcriptase and integrase. Skipper is the first example of a retrotransposon with a separate pro gene. Skipper is also novel in that it appears to use stop codon suppression rather than frameshifting to modulate pro expression. Finally, skipper and its components may provide useful tools for the genetic characterization of Dictyostelium. PMID:9518497

  19. Genomic distribution of copia-like transposable elements in somatic tissues and during development of Drosophila melanogaster.

    PubMed

    Di Franco, C; Pisano, C; Dimitri, P; Gigliotti, S; Junakovic, N

    1989-12-01

    The genomic distribution of elements of the copia, 412, B 104, mdg 1, mdg 4 and 1731 transposon families was compared by the Southern technique in DNA preparations extracted from brains, salivary glands and adult flies of two related Drosophila lines. The copia, 412 and mdg 1 sequences were also probed in DNA from sperm, embryos, and 1st and 2nd instar larvae. The homogeneity of the patterns observed shows that somatic transposition is unlikely to occur frequently. A correlation between mobility and the euchromatic or heterochromatic location of transposable elements is discussed. In addition, an explanation of the variable band intensities of transposable elements in Southern autoradiographs is proposed. PMID:2560696

  20. Convergent Evolution of Ribonuclease H in LTR Retrotransposons and Retroviruses

    PubMed Central

    Ustyantsev, Kirill; Novikova, Olga; Blinov, Alexander; Smyshlyaev, Georgy

    2015-01-01

    Ty3/Gypsy long terminals repeat (LTR) retrotransposons are structurally and phylogenetically close to retroviruses. Two notable structural differences between these groups of genetic elements are 1) the presence in retroviruses of an additional envelope gene, env, which mediates infection, and 2) a specific dual ribonuclease H (RNH) domain encoded by the retroviral pol gene. However, similar to retroviruses, many Ty3/Gypsy LTR retrotransposons harbor additional env-like genes, promoting concepts of the infective mode of these retrotransposons. Here, we provide a further line of evidence of similarity between retroviruses and some Ty3/Gypsy LTR retrotransposons. We identify that, together with their additional genes, plant Ty3/Gypsy LTR retrotransposons of the Tat group have a second RNH, as do retroviruses. Most importantly, we show that the resulting dual RNHs of Tat LTR retrotransposons and retroviruses emerged independently, providing strong evidence for their convergent evolution. The convergent resemblance of Tat LTR retrotransposons and retroviruses may indicate similar selection pressures acting on these diverse groups of elements and reveal potential evolutionary constraints on their structure. We speculate that dual RNH is required to accelerate retrotransposon evolution through increased rates of strand transfer events and subsequent recombination events. PMID:25605791

  1. Analysis of plant diversity with retrotransposon-based molecular markers

    PubMed Central

    Kalendar, R; Flavell, A J; Ellis, T H N; Sjakste, T; Moisy, C; Schulman, A H

    2011-01-01

    Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants. PMID:20683483

  2. Roles for retrotransposon insertions in human disease.

    PubMed

    Hancks, Dustin C; Kazazian, Haig H

    2016-01-01

    Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans. PMID:27158268

  3. Two retrotransposons maintain telomeres in Drosophila

    PubMed Central

    Pardue, M.-L.; Rashkova, S.; Casacuberta, E.; DeBaryshe, P.G.; George, J. A.; Traverse, K.L.

    2005-01-01

    Telomeres across the genus Drosophila are maintained, not by telomerase, but by two non-LTR retrotransposons, HeT-A and TART, that transpose specifically to chromosome ends. Successive transpositions result in long head-to-tail arrays of these elements. Thus Drosophila telomeres, like those produced by telomerase, consist of repeated sequences reverse transcribed from RNA templates. The Drosophila repeats, complete and 5′-truncated copies of HeT-A and TART, are more complex than telomerase repeats; nevertheless these evolutionary variants have functional similarities to the more common telomeres. Like other telomeres, the Drosophila arrays are dynamic, fluctuating around an average length that can be changed by changes in the genetic background. Several proteins that interact with telomeres in other species have been found to have homologues that interact with Drosophila telomeres. Although they have hallmarks of non-LTR retrotransposons, HeT-A and TART appear to have a special relationship to Drosophila. Their Gag proteins are efficiently transported into diploid nuclei where HeT-A Gag recruits TART Gag to chromosome ends. Gags of other non-LTR elements remain predominantly in the cytoplasm. These studies provide intriguing evolutionary links between telomeres and retrotransposable elements. PMID:16132810

  4. The first complete Mag family retrotransposons discovered in Drosophila.

    PubMed

    Glukhov, I A; Kotnova, A P; Stefanov, Y E; Ilyin, Y V

    2016-01-01

    A retrotransposon of the Mag family was found in the Drosophila simulans genome for the first time. We also identified novel transposable elements representing the Mag family in seven Drosophila species. The high similarity between the 3' and 5' long terminal repeats in the found copies of transposable elements indicates that their retrotransposition has occurred relatively recently. Thus, the Mag family of retrotransposons is quite common for the genus Drosophila. PMID:27025475

  5. Retrotransposons as regulators of gene expression.

    PubMed

    Elbarbary, Reyad A; Lucas, Bronwyn A; Maquat, Lynne E

    2016-02-12

    Transposable elements (TEs) are both a boon and a bane to eukaryotic organisms, depending on where they integrate into the genome and how their sequences function once integrated. We focus on two types of TEs: long interspersed elements (LINEs) and short interspersed elements (SINEs). LINEs and SINEs are retrotransposons; that is, they transpose via an RNA intermediate. We discuss how LINEs and SINEs have expanded in eukaryotic genomes and contribute to genome evolution. An emerging body of evidence indicates that LINEs and SINEs function to regulate gene expression by affecting chromatin structure, gene transcription, pre-mRNA processing, or aspects of mRNA metabolism. We also describe how adenosine-to-inosine editing influences SINE function and how ongoing retrotransposition is countered by the body's defense mechanisms. PMID:26912865

  6. LTR retrotransposons, handy hitchhikers of plant regulation and stress response.

    PubMed

    Grandbastien, Marie-Angèle

    2015-04-01

    LTR retrotransposons are major components of plant genomes. They are regulated by a diverse array of external stresses and tissue culture conditions, displaying finely tuned responses to these stimuli, mostly in the form of upregulation. Second to stress conditions and tissue culture, meristems are also permissive for LTR retrotransposon expression, suggesting that a dedifferentiated cell status may represent a frequent activating condition. LTR regions are highly plastic and contain regulatory motifs similar to those of cellular genes. The activation of LTR retrotransposons results from interplay between the release of epigenetic silencing and the recruitment by LTRs of specific regulatory factors. Despite the role of LTR retrotransposons in driving plant genome diversification, convincing evidence for major mobilizations of LTR retrotransposons remains much rarer than observations of massive bursts of transcriptional upregulation. Current evidence suggests that LTR retrotransposon expression may be involved in host functional plasticity, acting as dispersed regulatory modules able to redirect stress stimuli to adjacent plant genes. This may be of crucial importance for plants that cannot escape stress, and have evolved complex and highly coordinated responses to external challenges. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity. PMID:25086340

  7. Evidence of multiple retrotransposons in two litopenaeid species.

    PubMed

    Hizer, S E; Tamulis, W G; Robertson, L M; Garcia, D K

    2008-08-01

    Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes. The impact of the varied types of retrotransposons on these genomes is just beginning to be deciphered. In a step towards understanding their role in litopenaeid shrimp, we have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers designed from a RAPD-derived sequence. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. In silico searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains found in our PCR-derived sequences. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group that included five of our nine sequences. This group, which included elements from both L. stylirostris and L. vannamei, appeared most closely related to the highly active RTE clade. Our remaining four sequences placed in the CR1 and I clades of retrotransposons, with one showing strong similarity to ancient Penelope elements. This research describes three newly discovered retrotransposons in the L. stylirostris genome. Phylogenetic analysis clusters these in a monophyletic grouping with retrotransposons previously described from two closely related species, L. vannamei and Penaeus monodon. PMID:18557973

  8. Composite non-LTR retrotransposons in hominoid primates

    PubMed Central

    Damert, Annette

    2015-01-01

    Composite retrotransposons are widely distributed in the plant and animal kingdoms. Some of the most complex of these are found in hominoid primates. SVA, LAVA, PVA and FVA combine simple repeats, Alu fragments, a VNTR (Variable Number of Tandem Repeats) and variable 3′ domains, which are, except for PVA, derived from other retrotransposons. Although a likely precursor of SVA–a “tailed VNTR” named SVA2–had been identified in the Rhesus genome, the exact sequence and mechanism of the assembly of this type of composite retrotransposon had been elusive. The discovery of LAVA, PVA and FVA in gibbons provided the opportunity to delineate the order of assembly of the components of VNTR-containing retrotransposons. Our recent analysis suggests that an extinct “Alu-SVA2” acquired variant 3′ ends by splicing. In this commentary I will discuss the mode of assembly of VNTR composites in the context of their capacity to engage in alternative splicing to co-mobilize host RNA sequences and to become exonized. The second part will focus on structural determinants of VNTR composite retrotransposon mobilization in the context of lineage-specific expansion of particular families/subfamilies of these elements. PMID:26904376

  9. Genome-wide Annotation and Comparative Analysis of Long Terminal Repeat Retrotransposons between Pear Species of P. bretschneideri and P. Communis

    PubMed Central

    Yin, Hao; Du, Jianchang; Wu, Jun; Wei, Shuwei; Xu, Yingxiu; Tao, Shutian; Wu, Juyou; Zhang, Shaoling

    2015-01-01

    Recent sequencing of the Oriental pear (P. bretschneideri Rehd.) genome and the availability of the draft genome sequence of Occidental pear (P. communis L.), has provided a good opportunity to characterize the abundance, distribution, timing, and evolution of long terminal repeat retrotransposons (LTR-RTs) in these two important fruit plants. Here, a total of 7247 LTR-RTs, which can be classified into 148 families, have been identified in the assembled Oriental pear genome. Unlike in other plant genomes, approximately 90% of these elements were found to be randomly distributed along the pear chromosomes. Further analysis revealed that the amplification timeframe of elements varies dramatically in different families, super-families and lineages, and the Copia-like elements have highest activity in the recent 0.5 million years (Mys). The data also showed that two genomes evolved with similar evolutionary rates after their split from the common ancestor ~0.77–1.66 million years ago (Mya). Overall, the data provided here will be a valuable resource for further investigating the impact of transposable elements on gene structure, expression, and epigenetic modification in the pear genomes. PMID:26631625

  10. Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres.

    PubMed

    Liu, Zhao; Yue, Wei; Li, Dayong; Wang, Richard R-C; Kong, Xiuying; Lu, Kun; Wang, Guixiang; Dong, Yushen; Jin, Weiwei; Zhang, Xueyong

    2008-10-01

    Little is known of the dynamics of centromeric DNA in polyploid plants. We report the sequences of two centromere-associated bacterial artificial chromosome clones from a Triticum boeoticum library. Both autonomous and non-autonomous wheat centromeric retrotransposons (CRWs) were identified, both being closely associated with the centromeres of wheat. Fiber-fluorescence in situ hybridization and chromatin immunoprecipitation analysis showed that wheat centromeric retrotransposons (CRWs) represent a dominant component of the wheat centromere and are associated with centromere function. CRW copy number showed variation among different genomes: the D genome chromosomes contained fewer copies than either the A or B genome chromosomes. The frequency of lengthy continuous CRW arrays was higher than that in either rice or maize. The dynamics of CRWs and other retrotransposons at centromeric and pericentromeric regions during diploid speciation and polyploidization of wheat and its related species are discussed. PMID:18496705

  11. The diversity of retrotransposons and the properties of their reverse transcriptases.

    PubMed

    Eickbush, Thomas H; Jamburuthugoda, Varuni K

    2008-06-01

    A number of abundant mobile genetic elements called retrotransposons reverse transcribe RNA to generate DNA for insertion into eukaryotic genomes. Four major classes of retrotransposons are described here. First, the long-terminal-repeat (LTR) retrotransposons have similar structures and mechanisms to those of the vertebrate retroviruses. Genes that may enable these retrotransposons to leave a cell have been acquired by these elements in a number of animal and plant lineages. Second, the tyrosine recombinase retrotransposons are similar to the LTR retrotransposons except that they have substituted a recombinase for the integrase and recombine into the host chromosomes. Third, the non-LTR retrotransposons use a cleaved chromosomal target site generated by an encoded endonuclease to prime reverse transcription. Finally, the Penelope-like retrotransposons are not well understood but appear to also use cleaved DNA or the ends of chromosomes as primer for reverse transcription. Described in the second part of this review are the enzymatic properties of the reverse transcriptases (RTs) encoded by retrotransposons. The RTs of the LTR retrotransposons are highly divergent in sequence but have similar enzymatic activities to those of retroviruses. The RTs of the non-LTR retrotransposons have several unique properties reflecting their adaptation to a different mechanism of retrotransposition. PMID:18261821

  12. Yeast retrotransposon particles as antigen delivery systems.

    PubMed

    Kingsman, A J; Burns, N R; Layton, G T; Adams, S E

    1995-05-31

    The development of technologies to produce recombinant proteins for use in the pharmaceutical industry has made substantial advances, in particular in the area of generating antigens containing multiple copies of important immunological regions. One such antigen-carrier system is based on the ability of a protein encoded by the yeast retrotransposon, Ty, to self-assemble into virus-like particles. Ty-fusion proteins retain this ability to form particles, and a range of hybrid VLPs carrying a variety of heterologous antigens have been produced and shown to induce potent immune responses. In particular, hybrid VLPs carrying the core protein p24 of HIV (p24-VLPs) have been shown to induce antibody and T-cell proliferative responses in both experimental animals and human volunteers, and immunization of rabbits with VLPs carrying the principal neutralizing determinant of HIV (V3-VLPs) resulted in the induction of neutralizing antibody responses and T-cell proliferation. Further studies with V3-VLPs have shown that this particulate antigen stimulates enhanced V3-specific lymphoproliferative responses as compared to whole recombinant gp120 or to V3 peptide conjugated to albumin. The V3-VLPs also induce potent CTL responses following immunization of mice in the absence of adjuvant. These responses are MHC class I restricted and are mediated by CD8-positive cells. These observations therefore demonstrate that hybrid Ty-VLPs induce both humoral and cellular immune responses against HIV and suggest that these immunogens may be important in combatting AIDS and other infections. PMID:7625653

  13. Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration.

    PubMed

    Bridier-Nahmias, Antoine; Tchalikian-Cosson, Aurélie; Baller, Joshua A; Menouni, Rachid; Fayol, Hélène; Flores, Amando; Saïb, Ali; Werner, Michel; Voytas, Daniel F; Lesage, Pascale

    2015-05-01

    Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of RNA polymerase III (Pol III)-transcribed genes, yet the primary determinant of target specificity has remained elusive. Here we describe an interaction between Ty1 integrase and the AC40 subunit of Pol III and demonstrate that AC40 is the predominant determinant targeting Ty1 integration upstream of Pol III-transcribed genes. Lack of an integrase-AC40 interaction dramatically alters target site choice, leading to a redistribution of Ty1 insertions in the genome, mainly to chromosome ends. The mechanism of target specificity allows Ty1 to proliferate and yet minimizes genetic damage to its host. PMID:25931562

  14. Natural selection maintains the transcribed LTR retrotransposons in Nosema bombycis.

    PubMed

    Xiang, Heng; Pan, Guoqing; Zhang, Ruizhi; Xu, Jinshan; Li, Tian; Li, Wenle; Zhou, Zeyang; Xiang, Zhonghuai

    2010-05-01

    Eight intact LTR retrotransposons (Nbr1-Nbr8) have been previously characterized from the genome of Nosema bombycis, a eukaryotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements (Nbr9-Nbr14) identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions (Nbr12), deletions (Nbr11) and in-frame stop codons in coding regions (Nbr9) were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bombycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbr11 is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbr11 retrotransposon. Unlike other transposable elements, Nbr11 has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection. PMID:20513631

  15. Structure and Dynamics of Retrotransposons at Wheat Centromeres and Pericentromeres

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A centromere-associated bacterial artificial chromosome (BAC) clone TbBAC5, containing a 90 kb insert of Triticum boeoticum Boiss, genomic DNA, was fully sequenced. The Erika, Sukkula and Wgel-2 retrotransposons identified in TbBAC5 were A-genome rich in annual Triticeae. Southern analysis reveale...

  16. Plant centromeric retrotransposons: a structural and cytogenetic perspective

    PubMed Central

    2011-01-01

    Background The centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity. Results We have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD). A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active. Conclusions Comprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A). These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their transcriptional activity

  17. Retrotransposon- and microsatellite sequence-associated genomic changes in early 2 generations of a newly synthesized allotetraploid cucumis × hytivus Chen & Kirkbride

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Allopolyploidization is considered an essential evolutionary process in plants that could trigger genomic shock in allopolyploid genome through activation of transcription of retrotransposons, which may be important in plant evolution. Two retrotransposon-based markers, inter-retrotransposon amplifi...

  18. DIRS-1 and the other tyrosine recombinase retrotransposons.

    PubMed

    Poulter, R T M; Goodwin, T J D

    2005-01-01

    DIRS-1 is a retroelement from the slime mold Dictyostelium discoideum. Until recently only two related retrotransposons had been described: PAT from the nematode Panagrellus redivivus and Prt1 from the zygomycete fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these three elements suggested that they were closely related to each other and more distantly related to the Ty3/gypsy Long Terminal Repeat (LTR) retroelements. They have several unusual structural features that distinguish them from typical LTR elements. For instance, they each encode a tyrosine recombinase (YR), but not a DDE-type integrase or an aspartic protease. Although the DIRS-1-related elements are bordered by terminal repeats these differ from typical LTRs in a number of ways. In DIRS-1, for example, the terminal repeats are inverted (complementary), non-identical in sequence, and the outer edges of the terminal sequences are repeated (adjacent to each other) in the internal region. PAT has so-called "split" direct repeats in which the unrelated terminal sequences appear as direct repeats adjacent to each other in the internal region. The only repetition displayed by Prt1 is the presence of short inverted terminal repeats, but the sequenced copy of this element is believed to be a truncated version of an element with a structure resembling DIRS-1. The unusual structure of the terminal repeats of the DIRS1-like elements appears to be related to their replication via free circular intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. In recognition of these important distinctions it is proposed that the retrotransposons that encode tyrosine recombinases be called the tyrosine recombinase (or YR) retrotransposons. Recently a large number of additional YR retrotransposons have been described, including elements from fungi (zygomycetes and basidiomycetes), plants (green algae) and a

  19. Divergent long-terminal-repeat retrotransposon families in the genome of Paragonimus westermani

    PubMed Central

    Bae, Young-An

    2003-01-01

    To gain information on retrotransposons in the genome of Paragonimus westermani, PCR was carried out with degenerate primers, specific to protease and reverse transcriptase (rt) genes of long-terminal-repeat (LTR) retrotransposons. The PCR products were cloned and sequenced, after which 12 different retrotransposon-related sequences were isolated from the trematode genome. These showed various degrees of identity to the polyprotein of divergent retrotransposon families. A phylogenetic analysis demonstrated that these sequences could be classified into three different families of LTR retrotransposons, namely, Xena, Bel, and Gypsy families. Of these, two mRNA transcripts were detected by reverse transcriptase-PCR, showing that these two elements preserved their mobile activities. The genomic distributions of these two sequences were found to be highly repetitive. These results suggest that there are diverse retrotransposons including the ancient Xena family in the genome of P. westermani, which may have been involved in the evolution of the host genome. PMID:14699263

  20. Condensin II Subunit dCAP-D3 Restricts Retrotransposon Mobilization in Drosophila Somatic Cells

    PubMed Central

    Schuster, Andrew T.; Sarvepalli, Kavitha; Murphy, Eain A.; Longworth, Michelle S.

    2013-01-01

    Retrotransposon sequences are positioned throughout the genome of almost every eukaryote that has been sequenced. As mobilization of these elements can have detrimental effects on the transcriptional regulation and stability of an organism's genome, most organisms have evolved mechanisms to repress their movement. Here, we identify a novel role for the Drosophila melanogaster Condensin II subunit, dCAP-D3 in preventing the mobilization of retrotransposons located in somatic cell euchromatin. dCAP-D3 regulates transcription of euchromatic gene clusters which contain or are proximal to retrotransposon sequence. ChIP experiments demonstrate that dCAP-D3 binds to these loci and is important for maintaining a repressed chromatin structure within the boundaries of the retrotransposon and for repressing retrotransposon transcription. We show that dCAP-D3 prevents accumulation of double stranded DNA breaks within retrotransposon sequence, and decreased dCAP-D3 levels leads to a precise loss of retrotransposon sequence at some dCAP-D3 regulated gene clusters and a gain of sequence elsewhere in the genome. Homologous chromosomes exhibit high levels of pairing in Drosophila somatic cells, and our FISH analyses demonstrate that retrotransposon-containing euchromatic loci are regions which are actually less paired than euchromatic regions devoid of retrotransposon sequences. Decreased dCAP-D3 expression increases pairing of homologous retrotransposon-containing loci in tissue culture cells. We propose that the combined effects of dCAP-D3 deficiency on double strand break levels, chromatin structure, transcription and pairing at retrotransposon-containing loci may lead to 1) higher levels of homologous recombination between repeats flanking retrotransposons in dCAP-D3 deficient cells and 2) increased retrotransposition. These findings identify a novel role for the anti-pairing activities of dCAP-D3/Condensin II and uncover a new way in which dCAP-D3/Condensin II influences local

  1. Retrotransposon "Qian" mediated segmental duplication in silkworm, Bombyx mori.

    PubMed

    Xu, Yunmin; Jiang, Ning; Zou, Ziliang; Tu, Zhijian; Chen, Anli; Zhao, Qiaoling; Xiang, Zhonghuai; He, Ningjia

    2014-03-01

    Transposable elements constitute a large fraction of the eukaryotic genomes. They have the potential to alter genome structure and play a major role in genome evolution. Here, we report a segmental duplication mediated by a novel long terminal repeat (LTR) retrotransposon as the cause of an egg-shell recessive lethal mutant (l-em mutant) in silkworm (Bombyx mori). The segmental duplication resulted in the duplication of six genes and the disruption of two genes. Disruption of BmEP80 (B. mori egg protein 80), a gene encoding a major egg-shell structure protein, is likely responsible for the lethal water-loss phenotype in the l-em/l-em mutant. Our data revealed that BmEP80 is present in the inner egg-shell layer and plays important roles in resistance to water efflux form eggs. A novel LTR retrotransposon (named as "Qian") was identified and the model for the Qian-mediated chromosomal segmental duplication was proposed. Detail biochemical and genomic analyses on the l-em mutant offer an opportunity to demonstrate that an LTR retrotransposon could trigger duplication of a chromosomal segment (∼96.3 kb) and confer novel phenotype. PMID:24462715

  2. Retrotransposon profiling of RNA polymerase III initiation sites.

    PubMed

    Qi, Xiaojie; Daily, Kenneth; Nguyen, Kim; Wang, Haoyi; Mayhew, David; Rigor, Paul; Forouzan, Sholeh; Johnston, Mark; Mitra, Robi David; Baldi, Pierre; Sandmeyer, Suzanne

    2012-04-01

    Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold, some retrotransposons are associated with tRNA genes (tDNAs). In the Saccharomyces cerevisiae genome, the long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites of tDNAs. Ty1, 2, and 4 elements also cluster in the upstream regions of these genes. To determine the extent to which other Pol III-transcribed genes serve as genomic targets for Ty3, a set of 10,000 Ty3 genomic retrotranspositions were mapped using high-throughput DNA sequencing. Integrations occurred at all known tDNAs, two tDNA relics (iYGR033c and ZOD1), and six non-tDNA, Pol III-transcribed types of genes (RDN5, SNR6, SNR52, RPR1, RNA170, and SCR1). Previous work in vitro demonstrated that the Pol III transcription factor (TF) IIIB is important for Ty3 targeting. However, seven loci that bind the TFIIIB loader, TFIIIC, were not targeted, underscoring the unexplained absence of TFIIIB at those sites. Ty3 integrations also occurred in two open reading frames not previously associated with Pol III transcription, suggesting the existence of a small number of additional sites in the yeast genome that interact with Pol III transcription complexes. PMID:22287102

  3. Characterization of AFLAV, a Tfl/Sushi retrotransposon from Aspergillus flavus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The insert of pAF28 contains a 4.5 kb region which encodes a truncated retrotransposon (AfRTL-1). In search for a full-length and intact copy of retrotransposon, we exploited a novel PCR cloning strategy by amplifying a 3.4 kb region from the genomic DNA of A. flavus NRRL 6541. The fragment was cl...

  4. Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian.

    PubMed

    Cao, Liping; Yin, Guojun; Cao, Zheming; Bing, Xuwen; Ding, Weidong

    2016-06-01

    A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues. PMID:27178280

  5. DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm

    PubMed Central

    Jaligot, Estelle; Beulé, Thierry; Collin, Myriam; Agbessi, Mawussé D. T.; Sabot, François; Garsmeur, Olivier; D'Hont, Angélique; Alwee, Sharifah Shahrul Rabiah Syed; Rival, Alain

    2014-01-01

    The mantled floral phenotype of oil palm (Elaeis guineensis) affects somatic embryogenesis-derived individuals and is morphologically similar to mutants defective in the B-class MADS-box genes. This somaclonal variation has been previously demonstrated to be associated to a significant deficit in genome-wide DNA methylation. In order to elucidate the possible role of DNA methylation in the transcriptional regulation of EgDEF1, the APETALA3 ortholog of oil palm, we studied this epigenetic mark within the gene in parallel with transcript accumulation in both normal and mantled developing inflorescences. We also examined the methylation and expression of two neighboring retrotransposons that might interfere with EgDEF1 regulation. We show that the EgDEF1 gene is essentially unmethylated and that its methylation pattern does not change with the floral phenotype whereas expression is dramatically different, ruling out a direct implication of DNA methylation in the regulation of this gene. Also, we find that both the gypsy element inserted within an intron of the EgDEF1 gene and the copia element located upstream from the promoter are heavily methylated and show little or no expression. Interestingly, we identify a shorter, alternative transcript produced by EgDEF1 and characterize its accumulation with respect to its full-length counterpart. We demonstrate that, depending on the floral phenotype, the respective proportions of these two transcripts change differently during inflorescence development. We discuss the possible phenotypical consequences of this alternative splicing and the new questions it raises in the search for the molecular mechanisms underlying the mantled phenotype in the oil palm. PMID:24638102

  6. Diversity and varietal classification of Hibiscus syriacus L. with the heterogeneity within retrotransposon-like elements.

    PubMed

    Lee, Seung Jae; Jeung, Ji Ung; Cho, Sung Ki; Um, Bo Young; Chung, Won-Il; Bae, Jung Myung; Shin, Jeong Sheop

    2002-06-30

    Retrotransposons are present in multi-copy numbers that are integrated into plant genomes with considerable heterogeneous sequences within a single plant and between plant species, which allows the use of retrotransposons as additional sources of DNA polymorphism. A primer design for the sequence-tagged specific site and cleaved amplified polymorphic sequences (STS-CAPs) that are derived from retrotransposon-like sequences was developed for the molecular marker analysis in Hibiscus syriacus. This method was applied for the detection of sequence variations of intact retrotransposons that exist in plant genomes, which resulted in higher polymorphisms than in the amplified fragment length polymorphism (AFLP). Through STS-CAPs, specific fingerprinting data among H. syriacus varieties can be easily distinguished and generated with reproducible results. It could also be adapted to any species that possess multi-copy retrotransposons for varietal identification as well as the assessment of genetic relationships. PMID:12132574

  7. The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.

    PubMed

    Zuccolo, Andrea; Scofield, Douglas G; De Paoli, Emanuele; Morgante, Michele

    2015-08-15

    Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms. PMID:25982862

  8. LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

    PubMed Central

    Sun, Cheng; Shepard, Donald B.; Chong, Rebecca A.; López Arriaza, José; Hall, Kathryn; Castoe, Todd A.; Feschotte, Cédric; Pollock, David D.; Mueller, Rachel Lockridge

    2012-01-01

    Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders. PMID:22200636

  9. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting.

    PubMed

    Suzuki, Shunsuke; Ono, Ryuichi; Narita, Takanori; Pask, Andrew J; Shaw, Geoffrey; Wang, Changshan; Kohda, Takashi; Alsop, Amber E; Marshall Graves, Jennifer A; Kohara, Yuji; Ishino, Fumitoshi; Renfree, Marilyn B; Kaneko-Ishino, Tomoko

    2007-04-13

    Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10) is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii), but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus), suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR) associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 5' region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation. PMID:17432937

  10. Coevolution of the telomeric retrotransposons across Drosophila species.

    PubMed Central

    Casacuberta, Elena; Pardue, Mary-Lou

    2002-01-01

    As in other eukaryotes, telomeres in Drosophila melanogaster are composed of long arrays of repeated DNA sequences. Remarkably, in D. melanogaster these repeats are produced, not by telomerase, but by successive transpositions of two telomere-specific retrotransposons, HeT-A and TART. These are the only transposable elements known to be completely dedicated to a role in chromosomes, a finding that provides an opportunity for investigating questions about the evolution of telomeres, telomerase, and the transposable elements themselves. Recent studies of D. yakuba revealed the presence of HeT-A elements with precisely the same unusual characteristics as HeT-A(mel) although they had only 55% nucleotide sequence identity. We now report that the second element, TART, is also a telomere component in D. yakuba; thus, these two elements have been evolving together since before the separation of the melanogaster and yakuba species complexes. Like HeT-A(yak), TART(yak) is undergoing concerted sequence evolution, yet they retain the unusual features TART(mel) shares with HeT-A(mel). There are at least two subfamilies of TART(yak) with significantly different sequence and expression. Surprisingly, one subfamily of TART(yak) has >95% sequence identity with a subfamily of TART(mel) and shows similar transcription patterns. As in D. melanogaster, other retrotransposons are excluded from the D. yakuba terminal arrays studied to date. PMID:12136015

  11. LINE-1 Retrotransposons: Mediators of Somatic Variation in Neuronal Genomes?

    PubMed Central

    Singer, Tatjana; McConnell, Michael J.; Marchetto, Maria C.N.; Coufal, Nicole G.; Gage, Fred H.

    2010-01-01

    LINE-1 (L1) elements are retrotransposons that insert extra copies of themselves throughout the genome using a “copy and paste” mechanism. L1s have contributed ~20% to total human genome content and are able to influence chromosome integrity and gene expression upon reinsertion. Recent studies show that L1 elements are active and “jumping” during neuronal differentiation. New somatic L1 insertions may generate “genomic plasticity” in neurons by causing variation in genomic DNA sequences and by altering the transcriptome of individual cells. Thus, L1-induced variation may affect neuronal plasticity and behavior. Here, we discuss potential consequences of L1-induced neuronal diversity and propose that a mechanism generating diversity in the brain could broaden the spectrum of behavioral phenotypes that can originate from any single genome. PMID:20471112

  12. The Tnt1 Retrotransposon Escapes Silencing in Tobacco, Its Natural Host

    PubMed Central

    Hernández-Pinzón, Inmaculada; Cifuentes, Marta; Hénaff, Elizabeth; Santiago, Néstor; Espinás, M. Lluïsa; Casacuberta, Josep M.

    2012-01-01

    Retrotransposons' high capacity for mutagenesis is a threat that genomes need to control tightly. Transcriptional gene silencing is a general and highly effective control of retrotransposon expression. Yet, some retrotransposons manage to transpose and proliferate in plant genomes, suggesting that, as shown for plant viruses, retrotransposons can escape silencing. However no evidence of retrotransposon silencing escape has been reported. Here we analyze the silencing control of the tobacco Tnt1 retrotransposon and report that even though constructs driven by the Tnt1 promoter become silenced when stably integrated in tobacco, the endogenous Tnt1 elements remain active. Silencing of Tnt1-containing transgenes correlates with high DNA methylation and the inability to incorporate H2A.Z into their promoters, whereas the endogenous Tnt1 elements remain partially methylated at asymmetrical positions and incorporate H2A.Z upon induction. Our results show that the promoter of Tnt1 is a target of silencing in tobacco, but also that endogenous Tnt1 elements can escape this control and be expressed in their natural host. PMID:22479451

  13. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

    PubMed Central

    Lexa, Matej; Kejnovský, Eduard; Šteflová, Pavlína; Konvalinová, Helena; Vorlíčková, Michaela; Vyskot, Boris

    2014-01-01

    Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures—some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3′UTR (but were also present in 5′UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements. PMID:24106085

  14. Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants

    PubMed Central

    Iwata, Aiko; Gill, Navdeep; Jackson, Scott A.

    2012-01-01

    Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the Retrosat2 family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of Retrosat2. Unlike the ORF1, the ORF0 sequences from Retrosat2 and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, Retrosat2 and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of Retrosat2 homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species. PMID:23119066

  15. CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome.

    PubMed

    Göke, Jonathan; Ng, Huck Hui

    2016-08-01

    The human genome contains millions of fragments from retrotransposons-highly repetitive DNA sequences that were once able to "copy and paste" themselves to other regions in the genome. However, the majority of retrotransposons have lost this capacity through acquisition of mutations or through endogenous silencing mechanisms. Without this imminent threat of transposition, retrotransposons have the potential to act as a major source of genomic innovation. Indeed, large numbers of retrotransposons have been found to be active in specific contexts: as gene regulatory elements and promoters for protein-coding genes or long noncoding RNAs, among others. In this review, we summarise recent findings about retrotransposons, with implications in gene expression regulation, the expansion of gene isoform diversity and the generation of long noncoding RNAs. We highlight key examples that demonstrate their role in cellular identity and their versatility as markers of cell states, and we discuss how their dysregulation may contribute to the formation of and possibly therapeutic response in human cancers. PMID:27402545

  16. Retrotransposon Hypomethylation in Melanoma and Expression of a Placenta-Specific Gene

    PubMed Central

    Macaulay, Erin C.; Roberts, Hester E.; Cheng, Xi; Jeffs, Aaron R.; Baguley, Bruce C.; Morison, Ian M.

    2014-01-01

    In the human placenta, DNA hypomethylation permits the expression of retrotransposon-derived genes that are normally silenced by methylation in somatic tissues. We previously identified hypomethylation of a retrotransposon-derived transcript of the voltage-gated potassium channel gene KCNH5 that is expressed only in human placenta. However, an RNA sequence from this placental-specific transcript has been reported in melanoma. This study examined the promoter methylation and expression of the retrotransposon-derived KCNH5 transcript in 25 melanoma cell lines to determine whether the acquisition of ‘placental’ epigenetic marks is a feature of melanoma. Methylation and gene expression analysis revealed hypomethylation of this retrotransposon in melanoma cell lines, particularly in those samples that express the placental KCNH5 transcript. Therefore we propose that hypomethylation of the placental-specific KCNH5 promoter is frequently associated with KCNH5 expression in melanoma cells. Our findings show that melanoma can develop hypomethylation of a retrotransposon-derived gene; a characteristic notably shared with the normal placenta. PMID:24759919

  17. Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The proliferation of retrotransposons within a genome can contribute to increased sizes and affect the function of eukaryotic genes. BEL/Pao-like long-terminal repeat (LTR) retrotransposons were annotated from the highly adaptable insect species Diabrotica virgifera virgifera, the western corn root...

  18. New aspartic proteinase of Ulysses retrotransposon from Drosophila virilis.

    PubMed

    Volkov, D A; Dergousova, N I; Rumsh, L D

    2004-06-01

    This work is focused on the investigation of a proteinase of Ulysses mobile genetic element from Drosophila virilis. The primary structure of this proteinase is suggested based on comparative analysis of amino acid sequences of aspartic proteinases from retroviruses and retrotransposons. The corresponding cDNA fragment has been cloned and expressed in E. coli. The protein accumulated in inclusion bodies. The recombinant protein (12 kD) was subjected to refolding and purified by affinity chromatography on pepstatin-agarose. Proteolytic activity of the protein was determined using oligopeptide substrates melittin and insulin B-chain. It was found that the maximum of the proteolytic activity is displayed at pH 5.5 as for the majority of aspartic proteinases. We observed that hydrolysis of B-chain of insulin was totally inhibited by pepstatin A in the micromolar concentration range. The molecular weight of the monomer of the Ulysses proteinase was determined by MALDI-TOF mass-spectrometry. PMID:15236611

  19. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma.

    PubMed

    Rodić, Nemanja; Steranka, Jared P; Makohon-Moore, Alvin; Moyer, Allison; Shen, Peilin; Sharma, Reema; Kohutek, Zachary A; Huang, Cheng Ran; Ahn, Daniel; Mita, Paolo; Taylor, Martin S; Barker, Norman J; Hruban, Ralph H; Iacobuzio-Donahue, Christine A; Boeke, Jef D; Burns, Kathleen H

    2015-09-01

    Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed after the disease has metastasized; it is among the most lethal forms of cancer. We recently described aberrant expression of an open reading frame 1 protein, ORF1p, encoded by long interspersed element-1 (LINE-1; L1) retrotransposon, in PDAC. To test whether LINE-1 expression leads to somatic insertions of this mobile DNA, we used a targeted method to sequence LINE-1 insertion sites in matched PDAC and normal samples. We found evidence of 465 somatic LINE-1 insertions in 20 PDAC genomes, which were absent from corresponding normal samples. In cases in which matched normal tissue, primary PDAC and metastatic disease sites were available, insertions were found in primary and metastatic tissues in differing proportions. Two adenocarcinomas secondarily involving the pancreas, but originating in the stomach and duodenum, acquired insertions with a similar discordance between primary and metastatic sites. Together, our findings show that LINE-1 contributes to the genetic evolution of PDAC and suggest that somatic insertions are acquired discontinuously in gastrointestinal neoplasms. PMID:26259033

  20. LINE-1 retrotransposons: from 'parasite' sequences to functional elements.

    PubMed

    Paço, Ana; Adega, Filomena; Chaves, Raquel

    2015-02-01

    Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed. PMID:25106509

  1. Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

    PubMed Central

    Lee, Jungnam; Han, Kyudong; Meyer, Thomas J.; Kim, Heui-Soo; Batzer, Mark A.

    2008-01-01

    The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution. PMID:19112500

  2. Inter-retrotransposon-amplified polymorphism markers for germplasm characterization in Manihot esculenta (Euphorbiaceae).

    PubMed

    Oliveira-Silva, A M; Silva, G F; Dias, M C; Clement, C R; Sousa, N R

    2014-01-01

    Manioc, Manihot esculenta, is economically important in many tropical and subtropical countries. The genetic variability of the species has not been fully explored, and new information may help expand its use. Molecular markers based on retrotransposons have good potential for analysis of genetic diversity given their abundance in the genome. Eight long terminal repeat retrotransposons were selected for the development of inter-retrotransposon-amplified polymorphism markers. To test these primers, we analyzed 32 varieties from Anori, 30 from Manicoré and 10 Mandiocabas from the Manioc Germplasm Bank at Embrapa Western Amazonia. The six informative primer pairs yielded 20- 60 polymorphic bands, averaging 92% polymorphism (51.7-98.4) and 0.37 heterozygosity (0.17 to 0.40), with a Shannon information index of 0.54 (0.26-0.59). These markers can be used to explore the genetic diversity of manioc. PMID:24938466

  3. Insertion of Retrotransposons at Chromosome Ends: Adaptive Response to Chromosome Maintenance

    PubMed Central

    Servant, Geraldine; Deininger, Prescott L.

    2016-01-01

    The telomerase complex is a specialized reverse transcriptase (RT) that inserts tandem DNA arrays at the linear chromosome ends and contributes to the protection of the genetic information in eukaryotic genomes. Telomerases are phylogenetically related to retrotransposons, encoding also the RT activity required for the amplification of their sequences throughout the genome. Intriguingly the telomerase gene is lost from the Drosophila genome and tandem retrotransposons replace telomeric sequences at the chromosome extremities. This observation suggests the versatility of RT activity in counteracting the chromosome shortening associated with genome replication and that retrotransposons can provide this activity in case of a dysfunctional telomerase. In this review paper, we describe the major classes of retroelements present in eukaryotic genomes in order to point out the differences and similarities with the telomerase complex. In a second part, we discuss the insertion of retroelements at the ends of chromosomes as an adaptive response for dysfunctional telomeres. PMID:26779254

  4. DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes.

    PubMed

    Knisbacher, Binyamin A; Levanon, Erez Y

    2016-02-01

    Long terminal repeat retrotransposons (LTR) are widespread in vertebrates and their dynamism facilitates genome evolution. However, these endogenous retroviruses (ERVs) must be restricted to maintain genomic stability. The APOBECs, a protein family that can edit C-to-U in DNA, do so by interfering with reverse transcription and hypermutating retrotransposon DNA. In some cases, a retrotransposon may integrate into the genome despite being hypermutated. Such an event introduces a unique sequence into the genome, increasing retrotransposon diversity and the probability of developing new function at the locus of insertion. The prevalence of this phenomenon and its effects on vertebrate genomes are still unclear. In this study, we screened ERV sequences in the genomes of 123 diverse species and identified hundreds of thousands of edited sites in multiple vertebrate lineages, including placental mammals, marsupials, and birds. Numerous edited ERVs carry high mutation loads, some with greater than 350 edited sites, profoundly damaging their open-reading frames. For many of the species studied, this is the first evidence that APOBECs are active players in their innate immune system. Unexpectedly, some birds and especially zebra finch and medium ground-finch (one of Darwin's finches) are exceptionally enriched in DNA editing. We demonstrate that edited retrotransposons may be preferentially retained in active genomic regions, as reflected from their enrichment in genes, exons, promoters, and transcription start sites, thereby raising the probability of their exaptation for novel function. In conclusion, DNA editing of retrotransposons by APOBECs has a substantial role in vertebrate innate immunity and may boost genome evolution. PMID:26541172

  5. DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes

    PubMed Central

    Knisbacher, Binyamin A.; Levanon, Erez Y.

    2016-01-01

    Long terminal repeat retrotransposons (LTR) are widespread in vertebrates and their dynamism facilitates genome evolution. However, these endogenous retroviruses (ERVs) must be restricted to maintain genomic stability. The APOBECs, a protein family that can edit C-to-U in DNA, do so by interfering with reverse transcription and hypermutating retrotransposon DNA. In some cases, a retrotransposon may integrate into the genome despite being hypermutated. Such an event introduces a unique sequence into the genome, increasing retrotransposon diversity and the probability of developing new function at the locus of insertion. The prevalence of this phenomenon and its effects on vertebrate genomes are still unclear. In this study, we screened ERV sequences in the genomes of 123 diverse species and identified hundreds of thousands of edited sites in multiple vertebrate lineages, including placental mammals, marsupials, and birds. Numerous edited ERVs carry high mutation loads, some with greater than 350 edited sites, profoundly damaging their open-reading frames. For many of the species studied, this is the first evidence that APOBECs are active players in their innate immune system. Unexpectedly, some birds and especially zebra finch and medium ground-finch (one of Darwin’s finches) are exceptionally enriched in DNA editing. We demonstrate that edited retrotransposons may be preferentially retained in active genomic regions, as reflected from their enrichment in genes, exons, promoters, and transcription start sites, thereby raising the probability of their exaptation for novel function. In conclusion, DNA editing of retrotransposons by APOBECs has a substantial role in vertebrate innate immunity and may boost genome evolution. PMID:26541172

  6. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.

    PubMed

    Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H; Cavallini, Andrea; Natali, Lucia

    2015-12-01

    The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. PMID:26608057

  7. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes

    PubMed Central

    Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H.; Cavallini, Andrea; Natali, Lucia

    2015-01-01

    The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes—7 wild accessions and 8 cultivars—of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. PMID:26608057

  8. Somatic reversion of some copia-like induced mutations, at the white locus of Drosophila melanogaster, after treatment with alkylating agents.

    PubMed

    Soriano, S; Creus, A; Marcos, R; Xamena, N

    1995-01-01

    It has been suggested that transposable elements can be associated with different types of genotoxic effects. For this reason it seems appropriate to outline suitable systems to detect changes in the phenotypic expression of the loci containing transposable elements, as well as those agents that induce such changes. The sex-linked white locus offers a suitable experimental system for studying such events because most of the spontaneous mutations at the white locus are the result of insertions of repeated mobile sequences, and it is easy to follow mutational changes of the locus due to the possibility of detecting even slight changes in eye color. Here we report the results obtained in different strains of Drosophila melanogaster with copia-like induced mutations at the white locus, after treatment with three alkylating agents: ethyl methanesulfonate (EMS), methyl methanesulfonate (MMS), and N-nitroso-N-ethylurea (ENU). The three insertional white mutants used in this work were wa4, wbf, and wsp55, with the wa2 mutation used as control because its mutant phenotype is the result of a point mutation instead of the insertion of a DNA fragment. Our data constitute evidence that EMS, MMS, and ENU induce a clear increase in the frequencies of somatic-revertant sectors in the three strains carrying a white allele with an inserted copia-like element. For the wa2 strain, whose mutant phenotype is the result of a point mutation, only ENU at the highest concentration tested is able to induce a significant increase in the somatic reversion frequency. In addition, our results indicate that the use of D. melanogaster strains with transposable elements in the white locus is suitable for detecting genotoxic damage induced by chemicals. PMID:7698106

  9. Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons

    PubMed Central

    Shpiz, Sergey; Olovnikov, Ivan; Sergeeva, Anna; Lavrov, Sergey; Abramov, Yuri; Savitsky, Mikhail; Kalmykova, Alla

    2011-01-01

    In the Drosophila germline, retrotransposons are silenced by the PIWI-interacting RNA (piRNA) pathway. Telomeric retroelements HeT-A, TART and TAHRE, which are involved in telomere maintenance in Drosophila, are also the targets of piRNA-mediated silencing. We have demonstrated that expression of reporter genes driven by the HeT-A promoter is under the control of the piRNA silencing pathway independent of the transgene location. In order to test directly whether piRNAs affect the transcriptional state of retrotransposons we performed a nuclear run-on (NRO) assay and revealed increased density of the active RNA polymerase complexes at the sequences of endogenous HeT-A and TART telomeric retroelements as well as HeT-A-containing constructs in the ovaries of spn-E mutants and in flies with piwi knockdown. This strongly correlates with enrichment of two histone H3 modifications (dimethylation of lysine 79 and dimethylation of lysine 4), which mark transcriptionally active chromatin, on the same sequences in the piRNA pathway mutants. spn-E mutation and piwi knockdown results in transcriptional activation of some other non-telomeric retrotransposons in the ovaries, such as I-element and HMS Beagle. Therefore piRNA-mediated transcriptional mode of silencing is involved in the control of retrotransposon expression in the Drosophila germline. PMID:21764773

  10. Epigenetics and cortical spreading depression: changes of DNA methylation level at retrotransposon sequences.

    PubMed

    Drongitis, Denise; Rainone, Sara; Piscopo, Marina; Viggiano, Emanuela; Viggiano, Alessandro; De Luca, Bruno; Fucci, Laura; Donizetti, Aldo

    2016-08-01

    Cortical spreading depression (CSD) is an evolutionarily conserved phenomenon that involves a slow and self-propagating depolarization wave associated with spontaneous depression of electrical neuronal activity. CSD plays a central role in the pathophysiology of several brain diseases and is considered to be able to promote "Preconditioning". This phenomenon consists of the brain protecting itself against future injury by adaptation. Understanding of the molecular mechanisms underlying Preconditioning has significant clinical implications. We have already proposed that the long-lasting effects of CSD could be related to silencing of retrotransposon sequences by histone methylation. We analyzed DNA methylation of two retrotransposon sequences, LINE1 and L1, and their corresponding expression pattern after CSD induction. Based on immunoprecipitation assay of the methylated DNA (meDIP), we demonstrated hypermethylation of both sequences in preconditioned rat brain cortex compared with a control 24 h after CSD induction. Using quantitative PCR, we also showed that CSD induction caused a decrease of the transcript level of both retrotransposon sequences. Our data are consistent with the hypothesis of epigenetic modifications in Preconditioning-dependent neuroprotection by increasing genome stability via the silencing of retrotransposon sequences. PMID:27169424

  11. Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum.

    PubMed Central

    Vicient, CM; Suoniemi, A; Anamthawat-Jónsson, K; Tanskanen, J; Beharav, A; Nevo, E; Schulman, AH

    1999-01-01

    The replicative retrotransposon life cycle offers the potential for explosive increases in copy number and consequent inflation of genome size. The BARE-1 retrotransposon family of barley is conserved, disperse, and transcriptionally active. To assess the role of BARE-1 in genome evolution, we determined the copy number of its integrase, its reverse transcriptase, and its long terminal repeat (LTR) domains throughout the genus Hordeum. On average, BARE-1 contributes 13.7 x 10(3) full-length copies, amounting to 2.9% of the genome. The number increases with genome size. Two LTRs are associated with each internal domain in intact retrotransposons, but surprisingly, BARE-1 LTRs were considerably more prevalent than would be expected from the numbers of intact elements. The excess in LTRs increases as both genome size and BARE-1 genomic fraction decrease. Intrachromosomal homologous recombination between LTRs could explain the excess, removing BARE-1 elements and leaving behind solo LTRs, thereby reducing the complement of functional retrotransposons in the genome and providing at least a partial "return ticket from genomic obesity." PMID:10488242

  12. The Ty1 LTR-retrotransposon of budding yeast, Saccharomyces cerevisiae

    PubMed Central

    Curcio, M. Joan; Lutz, Sheila; Lesage, Pascale

    2015-01-01

    Summary Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses [1]. The Ty1 element of the budding yeast Saccharomyces cerevisiae was the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in the S. cerevisiae genome but also the ease and breadth of genomic, biochemical and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host co-factors known to influence retrotransposition and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology. PMID:25893143

  13. Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain.

    PubMed

    Weber, Beatrice; Schmidt, Thomas

    2009-01-01

    LTR retrotransposons belong to a major group of DNA sequences that are often localized in plant centromeres. Using BAC inserts originating from the centromere of a monosomic wild beet (Beta procumbens) chromosome fragment in Beta vulgaris, two complete LTR retrotransposons were identified. Both elements, designated Beetle1 and Beetle2, possess a coding region with genes in the order characteristic for Ty3-gypsy retrotransposons. Beetle1 and Beetle2 have a chromodomain in the C-terminus of the integrase gene and are highly similar to the centromeric retrotransposons (CRs) of rice, maize, and barley. Both retroelements were localized in the centromeric region of B. procumbens chromosomes by fluorescence in-situ hybridization. They can therefore be classified as centromere-specific chromoviruses. PCR analysis using RNA as template indicated that Beetle1 and Beetle2 are transcriptionally active. On the basis of the sequence diversity between the LTR sequences, it was estimated that Beetle1 and Beetle2 transposed within the last 60,000 years and 130,000 years, respectively. The centromeric localization of Beetle1 and Beetle2 and their transcriptional activity combined with high sequence conservation within each family play an important structural role in the centromeres of B. procumbens chromosomes. PMID:19322668

  14. Molecular characterization and genomic distribution of Isis: a new retrotransposon of Drosophila buzzatii.

    PubMed

    García Guerreiro, M P; Fontdevila, A

    2007-01-01

    A new transposable element, Isis, is identified as a LTR retrotransposon in Drosophila buzzatii. DNA sequence analysis shows that Isis contains three long ORFs similar to gag, pol and env genes of retroviruses. The ORF1 exhibits sequence homology to matrix, capsid and nucleocapsid gag proteins and ORF2 encodes a putative protease (PR), a reverse transcriptase (RT), an Rnase H (RH) and an integrase (IN) region. The analysis of a putative env product, encoded by the env ORF3, shows a degenerated protein containing several stop codons. The molecular study of the putative proteins coded by this new element shows striking similarities to both Ulysses and Osvaldo elements, two LTR retrotransposons, present in D. virilis and D. buzzatii, respectively. Comparisons of the predicted Isis RT to several known retrotransposons show strong phylogenetic relationships to gypsy-like elements, particulary to Ulysses retrotransposon. Studies of Isis chromosomal distribution show a strong hybridization signal in centromeric and pericentromeric regions, and a scattered distribution along all chromosomal arms. The existence of insertional polymorphisms between different strains and high molecular weight bands by Southern blot suggests the existence of full-sized copies that have been active recently. The presence of euchromatic insertion sites coincident between Isis and Osvaldo could indicate preferential insertion sites of Osvaldo element into Isis sequence or vice versa. Moreover, the presence of Isis in different species of the buzzatii complex indicates the ancient origin of this element. PMID:17039376

  15. The dingo non-long terminal repeat retrotransposons from the genome of the hookworm, Ancylostoma caninum.

    PubMed

    Laha, Thewarach; Kewgrai, Nonglack; Loukas, Alex; Brindley, Paul J

    2006-07-01

    Members of the retrotransposable element (RTE) clade of non-long terminal repeat (LTR) retrotransposon are widely distributed among eukaryote taxa, with representatives known from Caenorhabditis elegans, mammals, mosquitoes, schistosomes, and other taxa. An RTE retrotransposon has not, however, been characterized in detail from a parasitic nematode. Here, we characterize two discrete copies of an RTE-like non-LTR retrotransposon from the genome of the dog hookworm, Ancylostoma caninum. The elements were named dingo-1 and dingo-2. The full-length dingo-1 and dingo-2 elements were 3421 and 3171bp in length, respectively. They exhibited 54% nucleotide sequence identity to one another across their entire length and 40%/58% amino-acid sequence identity/similarity across their open reading frames. dingo-1 and dingo-2 exhibited hallmark structures and sequences of non-LTR retrotransposons of the RTE family including a single open reading frame encoding apurinic-apyrimidinic endonuclease (EN) and reverse transcriptase (RT), in that order. Phylogenetic analyses targeting the RT and the EN domains both confirmed that dingo-1 and dingo-2 were members of the RTE clade and that they were closely related to RTE-1 from C. elegans, to BDDF from Bos taurus and to SR2 from Schistosoma mansoni. Dot blot hybridization indicated that as many as 100-1000 copies of dingo-1 reside within the genome of A. caninum, while detection by RT-PCR of transcripts encoding dingo-like elements suggested that dingo-1 and -2 may be retrotranspositionally active within the genome of A. caninum. The dingo elements are the first retrotransposons to be characterized from a hookworm genome. PMID:16445914

  16. Effects of As2O3 on DNA methylation, genomic instability, and LTR retrotransposon polymorphism in Zea mays.

    PubMed

    Erturk, Filiz Aygun; Aydin, Murat; Sigmaz, Burcu; Taspinar, M Sinan; Arslan, Esra; Agar, Guleray; Yagci, Semra

    2015-12-01

    Arsenic is a well-known toxic substance on the living organisms. However, limited efforts have been made to study its DNA methylation, genomic instability, and long terminal repeat (LTR) retrotransposon polymorphism causing properties in different crops. In the present study, effects of As2O3 (arsenic trioxide) on LTR retrotransposon polymorphism and DNA methylation as well as DNA damage in Zea mays seedlings were investigated. The results showed that all of arsenic doses caused a decreasing genomic template stability (GTS) and an increasing Random Amplified Polymorphic DNAs (RAPDs) profile changes (DNA damage). In addition, increasing DNA methylation and LTR retrotransposon polymorphism characterized a model to explain the epigenetically changes in the gene expression were also found. The results of this experiment have clearly shown that arsenic has epigenetic effect as well as its genotoxic effect. Especially, the increasing of polymorphism of some LTR retrotransposon under arsenic stress may be a part of the defense system against the stress. PMID:26396013

  17. An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons

    PubMed Central

    Jacobs, Frank MJ; Greenberg, David; Nguyen, Ngan; Haeussler, Maximilian; Ewing, Adam D; Katzman, Sol; Paten, Benedict; Salama, Sofie R; Haussler, David

    2014-01-01

    Summary Throughout evolution, primate genomes have been modified by waves of retrotransposon insertions1,2,3. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells (mESCs), transcriptional silencing of retrotransposons requires TRIM28 (KAP1) and it’s repressive complex, which can be recruited to target sites by KRAB zinc finger proteins such as murine-specific ZFP809 which binds to integrated murine leukemia virus DNA elements and recruits KAP1 to repress them4,5. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons6,7. However, the identity of KZNF genes battling retrotransposons currently active in the human genome, such as SINE-VNTR-Alu (SVA)8 and Long Interspersed Nuclear Element-1 (L1)9, is unknown. We find that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 MYA that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until ~12.5 MYA when the L1PA3-subfamily escaped ZNF93’s restriction through purge of the ZNF93 binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes. PMID:25274305

  18. A new non-LTR retrotransposon provides evidence for multiple distinct site-specific elements in Crithidia fasciculata miniexon arrays.

    PubMed Central

    Teng, S C; Wang, S X; Gabriel, A

    1995-01-01

    We have identified a new member of the family of trypanosome site-specific retrotransposons, using a degenerate oligonucleotide PCR strategy. The 9595 bp element, termed Crithidia retrotransposable element 2 (CRE2), was cloned and found to be inserted in the tandemly arrayed miniexon genes of Crithidia fasciculata. The element is flanked by 29 bp target site duplications but lacks the 3' poly dA tract characteristic of most other non-long terminal repeat retrotransposons. The amino terminal region of the single 2518-codon open reading frame contains a putative metal-binding motif and a proline-rich region similar to gag-like domains of other retrotransposons. The carboxy terminal region of this open reading frame shares sequence homology with the reverse transcriptase and putative endonuclease regions of three previously described trypanosomatid site-specific retrotransposons. All four of these retrotransposons are specifically inserted between nucleotides 11 and 12 of the highly conserved 39mer sequence of the miniexon gene. Most copies of CRE2 and the previously characterized CRE1 are located on different sized chromosomes. Additional CRE-related sequences were identified by screening Crithidia libraries. These results suggest that a particular sequence in the C. fasciculata miniexon repeat is the target for multiple distinct site-specific retrotransposon insertions. Images PMID:7659515

  19. Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences

    PubMed Central

    Kapitonov, Vladimir V.; Tempel, Sébastien; Jurka, Jerzy

    2009-01-01

    Rapidly growing number of sequenced genomes requires fast and accurate computational tools for analysis of different transposable elements (TEs). In this paper we focus on rapid and reliable procedure for classification of autonomous non-LTR retrotransposons based on alignment and clustering of their reverse transcriptase (RT) domains. Typically, the RT domain protein sequences encoded by different non-LTR retrotransposons are similar to each other in terms of significant BLASTP E-values. Therefore, they can be easily detected by the routine BLASTP searches of genomic DNA sequences coding for proteins similar to the RT domains of known non-LTR retrotransposons. However, detailed classification of non-LTR retrotransposons, i.e. their assignment to specific clades, is a slow and complex procedure that is not formalized or integrated as a standard set of computational methods and data. Here we describe a tool (RTclass1) designed for the fast and accurate automated assignment of novel non-LTR retrotransposons to known or novel clades using phylogenetic analysis of the RT domain protein sequences. RTclass1 classifies a particular non-LTR retrotransposon based on its RT domain in less than 10 minutes on a standard desktop computer and achieves 99.5% accuracy. RT1class1 works either as a standalone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1). PMID:19651192

  20. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers.

    PubMed

    Smýkal, P; Bačová-Kerteszová, N; Kalendar, R; Corander, J; Schulman, A H; Pavelek, M

    2011-05-01

    Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70-100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics. PMID:21293839

  1. Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution

    PubMed Central

    Vitte, Clémentine; Bennetzen, Jeffrey L.

    2006-01-01

    Analysis of LTR retrotransposon structures in five diploid angiosperm genomes uncovered very different relative levels of different types of genomic diversity. All species exhibited recent LTR retrotransposon mobility and also high rates of DNA removal by unequal homologous recombination and illegitimate recombination. The larger plant genomes contained many LTR retrotransposon families with >10,000 copies per haploid genome, whereas the smaller genomes contained few or no LTR retrotransposon families with >1,000 copies, suggesting that this differential potential for retroelement amplification is a primary factor in angiosperm genome size variation. The average ratios of transition to transversion mutations (Ts/Tv) in diverging LTRs were >1.5 for each species studied, suggesting that these elements are mostly 5-methylated at cytosines in an epigenetically silenced state. However, the diploid wheat Triticum monococcum and barley have unusually low Ts/Tv values (respectively, 1.9 and 1.6) compared with maize (3.9), medicago (3.6), and lotus (2.5), suggesting that this silencing is less complete in the two Triticeae. Such characteristics as the ratios of point mutations to indels (insertions and deletions) and the relative efficiencies of DNA removal by unequal homologous recombination compared with illegitimate recombination were highly variable between species. These latter variations did not correlate with genome size or phylogenetic relatedness, indicating that they frequently change during the evolutionary descent of plant lineages. In sum, the results indicate that the different sizes, contents, and structures of angiosperm genomes are outcomes of the same suite of mechanistic processes, but acting with different relative efficiencies in different plant lineages. PMID:17101966

  2. [Retrotransposon MDG4 and its role in genetic instability of a mutator strain of Drosophila melanogaster].

    PubMed

    Liubomirskaia, N V; Kim, A I; Il'in, Iu V

    2003-02-01

    This article summarizes the results of a ten-year study of genetic instability of a mutator strain of Drosophila melanogaster caused by transposition of the gypsy retrotransposon. The results of other authors working with an analogous system are analyzed. Possible mechanisms are suggested for the interaction of gypsy with the cell gene flamenco that participates in transposition control of this mobile element. PMID:12669411

  3. Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat.

    PubMed

    Senerchia, Natacha; Wicker, Thomas; Felber, François; Parisod, Christian

    2013-01-01

    Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindrica and Ae. geniculata using 454 identified more than 70% of the sequences as known TEs, mainly long terminal repeat (LTR) retrotransposons. Comparing the abundance of reads as well as patterns of sequence diversity and divergence within and among genomes assessed the dynamics of 44 major LTR retrotransposon families of the 165 identified. In particular, molecular population genetics on individual TE copies distinguished recently active from quiescent families and highlighted different evolutionary trajectories of retrotransposons among related species. This work presents a suite of tools suitable for current sequencing data, allowing to address the genome-wide evolutionary dynamics of TEs at the family level and advancing our understanding of the evolution of nonmodel genomes. PMID:23595021

  4. Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons.

    PubMed

    Qi, L L; Wu, J J; Friebe, B; Qian, C; Gu, Y Q; Fu, D L; Gill, B S

    2013-08-01

    Brachypodium distachyon is a wild annual grass belonging to the Pooideae, more closely related to wheat, barley, and forage grasses than rice and maize. As an experimental model, the completed genome sequence of B. distachyon provides a unique opportunity to study centromere evolution during the speciation of grasses. Centromeric satellite sequences have been identified in B. distachyon, but little is known about centromeric retrotransposons in this species. In the present study, bacterial artificial chromosome (BAC)-fluorescence in situ hybridization was conducted in maize, rice, barley, wheat, and rye using B. distachyon (Bd) centromere-specific BAC clones. Eight Bd centromeric BAC clones gave no detectable fluorescence in situ hybridization (FISH) signals on the chromosomes of rice and maize, and three of them also did not yield any FISH signals in barley, wheat, and rye. In addition, four of five Triticeae centromeric BAC clones did not hybridize to the B. distachyon centromeres, implying certain unique features of Brachypodium centromeres. Analysis of Brachypodium centromeric BAC sequences identified a long terminal repeat (LTR)-centromere retrotransposon of B. distachyon (CRBd1). This element was found in high copy number accounting for 1.6 % of the B. distachyon genome, and is enriched in Brachypodium centromeric regions. CRBd1 accumulated in active centromeres, but was lost from inactive ones. The LTR of CRBd1 appears to be specific to B. distachyon centromeres. These results reveal different evolutionary events of this retrotransposon family across grass species. PMID:23955173

  5. Restriction of Retrotransposon Mobilization in Schizosaccharomyces pombe by Transcriptional Silencing and Higher-Order Chromatin Organization

    PubMed Central

    Murton, Heather E.; Grady, Patrick J. R.; Chan, Tsun Ho; Cam, Hugh P.; Whitehall, Simon K.

    2016-01-01

    Uncontrolled propagation of retrotransposons is potentially detrimental to host genome integrity. Therefore, cells have evolved surveillance mechanisms to restrict the mobility of these elements. In Schizosaccharomyces pombe the Tf2 LTR retrotransposons are transcriptionally silenced and are also clustered in the nucleus into structures termed Tf bodies. Here we describe the impact of silencing and clustering on the mobility of an endogenous Tf2 element. Deletion of genes such as set1+ (histone H3 lysine 4 methyltransferase) or abp1+ (CENP-B homolog) that both alleviate silencing and clustering, result in a corresponding increase in mobilization. Furthermore, expression of constitutively active Sre1, a transcriptional activator of Tf2 elements, also alleviates clustering and induces mobilization. In contrast, clustering is not disrupted by loss of the HIRA histone chaperone, despite high levels of expression, and in this background, mobilization frequency is only marginally increased. Thus, mutations that compromise transcriptional silencing but not Tf bodies are insufficient to drive mobilization. Furthermore, analyses of mutant alleles that separate the transcriptional repression and clustering functions of Set1 are consistent with control of Tf2 propagation via a combination of silencing and spatial organization. Our results indicate that host surveillance mechanisms operate at multiple levels to restrict Tf2 retrotransposon mobilization. PMID:27343236

  6. Retrotransposon-based molecular markers for analysis of genetic diversity within the Genus Linum.

    PubMed

    Melnikova, Nataliya V; Kudryavtseva, Anna V; Zelenin, Alexander V; Lakunina, Valentina A; Yurkevich, Olga Yu; Speranskaya, Anna S; Dmitriev, Alexey A; Krinitsina, Anastasia A; Belenikin, Maxim S; Uroshlev, Leonid A; Snezhkina, Anastasiya V; Sadritdinova, Asiya F; Koroban, Nadezda V; Amosova, Alexandra V; Samatadze, Tatiana E; Guzenko, Elena V; Lemesh, Valentina A; Savilova, Anastasya M; Rachinskaia, Olga A; Kishlyan, Natalya V; Rozhmina, Tatiana A; Bolsheva, Nadezhda L; Muravenko, Olga V

    2014-01-01

    SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

  7. Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum

    PubMed Central

    Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Zelenin, Alexander V.; Lakunina, Valentina A.; Yurkevich, Olga Yu.; Speranskaya, Anna S.; Dmitriev, Alexey A.; Krinitsina, Anastasia A.; Belenikin, Maxim S.; Uroshlev, Leonid A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Koroban, Nadezda V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Guzenko, Elena V.; Lemesh, Valentina A.; Savilova, Anastasya M.; Rachinskaia, Olga A.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Bolsheva, Nadezhda L.; Muravenko, Olga V.

    2014-01-01

    SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

  8. Links between human LINE-1 retrotransposons and hepatitis virus-related hepatocellular carcinoma

    NASA Astrophysics Data System (ADS)

    Honda, Tomoyuki

    2016-05-01

    Hepatocellular carcinoma (HCC) accounts for approximately 80% of liver cancers, the third most frequent cause of cancer mortality. The most prevalent risk factors for HCC are infections by hepatitis B or hepatitis C virus. Findings suggest that hepatitis virus-related HCC might be a cancer in which LINE-1 retrotransposons, often termed L1, activity plays a potential role. Firstly, hepatitis viruses can suppress host defense factors that also control L1 mobilization. Secondly, many recent studies also have indicated that hypomethylation of L1 affects the prognosis of HCC patients. Thirdly, endogenous L1 retrotransposition was demonstrated to activate oncogenic pathways in HCC. Fourthly, several L1 chimeric transcripts with host or viral genes are found in hepatitis virus-related HCC. Such lines of evidence suggest a linkage between L1 retrotransposons and hepatitis virus-related HCC. Here, I briefly summarize current understandings of the association between hepatitis virus-related HCC and L1. Then, I discuss potential mechanisms of how hepatitis viruses drive the development of HCC via L1 retrotransposons. An increased understanding of the contribution of L1 to hepatitis virus-related HCC may provide unique insights related to the development of novel therapeutics for this disease.

  9. Three retrotransposon families in the genome of Giardia lamblia: Two telomeric, one dead

    PubMed Central

    Arkhipova, Irina R.; Morrison, Hilary G.

    2001-01-01

    Transposable elements inhabiting eukaryotic genomes are generally regarded either as selfish DNA, which is selectively neutral to the host organism, or as parasitic DNA, deleterious to the host. Thus far, the only agreed-upon example of beneficial eukaryotic transposons is provided by Drosophila telomere-associated retrotransposons, which transpose directly to the chromosome ends and thereby protect them from degradation. This article reports the transposon content of the genome of the protozoan Giardia lamblia, one of the earliest-branching eukaryotes. A total of three non-long terminal repeat retrotransposon families have been identified, two of which are located at the ends of chromosomes, and the third one contains exclusively dead copies with multiple internal deletions, nucleotide substitutions, and frame shifts. No other reverse transcriptase- or transposase-related sequences were found. Thus, the entire genome of this protozoan, which is not known to reproduce sexually, contains only retrotransposons that are either confined to telomeric regions and possibly beneficial, or inactivated and completely nonfunctional. PMID:11734649

  10. Links between Human LINE-1 Retrotransposons and Hepatitis Virus-Related Hepatocellular Carcinoma

    PubMed Central

    Honda, Tomoyuki

    2016-01-01

    Hepatocellular carcinoma (HCC) accounts for approximately 80% of liver cancers, the third most frequent cause of cancer mortality. The most prevalent risk factors for HCC are infections by hepatitis B or hepatitis C virus. Findings suggest that hepatitis virus-related HCC might be a cancer in which LINE-1 retrotransposon, often termed L1, activity plays a potential role. Firstly, hepatitis viruses can suppress host defense factors that also control L1 mobilization. Secondly, many recent studies also have indicated that hypomethylation of L1 affects the prognosis of HCC patients. Thirdly, endogenous L1 retrotransposition was demonstrated to activate oncogenic pathways in HCC. Fourthly, several L1 chimeric transcripts with host or viral genes are found in hepatitis virus-related HCC. Such lines of evidence suggest a linkage between L1 retrotransposons and hepatitis virus-related HCC. Here, I briefly summarize current understandings of the association between hepatitis virus-related HCC and L1. Then, I discuss potential mechanisms of how hepatitis viruses drive the development of HCC via L1 retrotransposons. An increased understanding of the contribution of L1 to hepatitis virus-related HCC may provide unique insights related to the development of novel therapeutics for this disease. PMID:27242996

  11. Restriction of Retrotransposon Mobilization in Schizosaccharomyces pombe by Transcriptional Silencing and Higher-Order Chromatin Organization.

    PubMed

    Murton, Heather E; Grady, Patrick J R; Chan, Tsun Ho; Cam, Hugh P; Whitehall, Simon K

    2016-08-01

    Uncontrolled propagation of retrotransposons is potentially detrimental to host genome integrity. Therefore, cells have evolved surveillance mechanisms to restrict the mobility of these elements. In Schizosaccharomyces pombe the Tf2 LTR retrotransposons are transcriptionally silenced and are also clustered in the nucleus into structures termed Tf bodies. Here we describe the impact of silencing and clustering on the mobility of an endogenous Tf2 element. Deletion of genes such as set1(+) (histone H3 lysine 4 methyltransferase) or abp1(+) (CENP-B homolog) that both alleviate silencing and clustering, result in a corresponding increase in mobilization. Furthermore, expression of constitutively active Sre1, a transcriptional activator of Tf2 elements, also alleviates clustering and induces mobilization. In contrast, clustering is not disrupted by loss of the HIRA histone chaperone, despite high levels of expression, and in this background, mobilization frequency is only marginally increased. Thus, mutations that compromise transcriptional silencing but not Tf bodies are insufficient to drive mobilization. Furthermore, analyses of mutant alleles that separate the transcriptional repression and clustering functions of Set1 are consistent with control of Tf2 propagation via a combination of silencing and spatial organization. Our results indicate that host surveillance mechanisms operate at multiple levels to restrict Tf2 retrotransposon mobilization. PMID:27343236

  12. LINE-1 retrotransposons and let-7 miRNA: partners in the pathogenesis of cancer?

    PubMed Central

    Ohms, Stephen; Lee, Sung-Hun; Rangasamy, Danny

    2014-01-01

    Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are insertional mutagens capable of altering the genomic landscape in many ways. Activation of the normally silent LINE-1 retrotransposon is associated with a high level of cancer-associated DNA damage and genomic instability. Studies of LINE-1 have so far focused mainly on changes in gene expression, and our knowledge of its impact on functional non-coding RNAs is in its infancy. However, current evidence suggests that a significant number of human miRNAs originate from retrotransposon sequences. Furthermore, LINE-1 is generally not expressed in normal tissues while its expression is widespread in epithelial cancers. Based on our recent studies, we demonstrate a functional link between aberrant LINE-1 expression and deregulation of let-7 miRNA expression. Since the expression of let-7 is modulated by LINE-1 activity, we discuss possible mechanisms for this effect and how the silencing of LINE-1 activation could provide new therapeutic options for cancer treatment. Based on the deep sequencing of small RNAs in parallel with gene expression profiling in breast cancer cells, we have identified potential pathways linking L1 activity to let-7 processing and maturation and ultimately to the control of stemness in human cancer cells. PMID:25339972

  13. Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta).

    PubMed

    Kuhn, B C; Mangolin, C A; Souto, E R; Vicient, C M; Machado, M F P S

    2016-01-01

    Retrotransposons are abundant in the genomes of plants. In the present study, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers were developed for the cassava genome (Manihot esculenta Crantz). Four cassava cultivars (Fécula Branca, IPR-União, Olho Junto, and Tamboara, two samples per cultivar) were used to obtain IRAP and REMAP fingerprints. Twelve designed primers were amplified alone and in combinations. The 42 IRAP/REMAP primer combinations amplified 431 DNA segments (bands; markers) of which 36 (8.36%) were polymorphic. The largest number of informative markers (16) was detected using the primers AYF2 and AYF2xAYF4. The number of bands for each primer varied from 3 to 16, with an average of 10.26 amplified segments per primer. The size of the amplified products ranged between 100 and 7000 bp. The AYF2 primer generated the highest number of amplified segments and showed the highest number of polymorphic bands (68.75%). Two samples of each cassava cultivar were used to illustrate the usefulness and the polymorphism of IRAP/REMAP markers. IRAP and REMAP markers produced a high number of reproducible bands, and might be informative and reliable for investigation of genetic diversity and relationships among cassava cultivars. PMID:27173210

  14. Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment.

    PubMed

    Yıldız, M; Koçak, M; Baloch, F S

    2015-01-01

    Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra. PMID:26400290

  15. Transposable Element Proliferation and Genome Expansion Are Rare in Contemporary Sunflower Hybrid Populations Despite Widespread Transcriptional Activity of LTR Retrotransposons

    PubMed Central

    Kawakami, Takeshi; Dhakal, Preeti; Katterhenry, Angela N.; Heatherington, Chelsea A.; Ungerer, Mark C.

    2011-01-01

    Hybridization is a natural phenomenon that has been linked in several organismal groups to transposable element derepression and copy number amplification. A noteworthy example involves three diploid annual sunflower species from North America that have arisen via ancient hybridization between the same two parental taxa, Helianthus annuus and H. petiolaris. The genomes of the hybrid species have undergone large-scale increases in genome size attributable to long terminal repeat (LTR) retrotransposon proliferation. The parental species that gave rise to the hybrid taxa are widely distributed, often sympatric, and contemporary hybridization between them is common. Natural H. annuus × H. petiolaris hybrid populations likely served as source populations from which the hybrid species arose and, as such, represent excellent natural experiments for examining the potential role of hybridization in transposable element derepression and proliferation in this group. In the current report, we examine multiple H. annuus × H. petiolaris hybrid populations for evidence of genome expansion, LTR retrotransposon copy number increases, and LTR retrotransposon transcriptional activity. We demonstrate that genome expansion and LTR retrotransposon proliferation are rare in contemporary hybrid populations, despite independent proliferation events that took place in the genomes of the ancient hybrid species. Interestingly, LTR retrotransposon lineages that proliferated in the hybrid species genomes remain transcriptionally active in hybrid and nonhybrid genotypes across the entire sampling area. The finding of transcriptional activity but not copy number increases in hybrid genotypes suggests that proliferation and genome expansion in contemporary hybrid populations may be mitigated by posttranscriptional mechanisms of repression. PMID:21282712

  16. Reconstructing the evolutionary history of gypsy retrotransposons in the Périgord black truffle (Tuber melanosporum Vittad.).

    PubMed

    Payen, Thibaut; Murat, Claude; Martin, Francis

    2016-08-01

    Truffles are ascomycete fungi belonging to genus Tuber, and they form ectomycorrhizal associations with trees and shrubs. Transposable elements constitute more than 50 % of the black Périgord truffle (Tuber melanosporum) genome, which are mainly class 1 gypsy retrotransposons, but their impact on its genome is unknown. The aims of this study are to investigate the diversity of gypsy retrotransposons in this species and their evolutionary history by analysing the reference genome and six resequenced genomes of different geographic accessions. Using the reverse transcriptase sequences, six different gypsy retrotransposon clades were identified. Tmt1 and Tmt6 are the most abundant transposable elements, representing 14 and 13 % of the T. melanosporum genome, respectively. Tmt6 showed a major burst of proliferation between 1 and 4 million years ago, but evidence of more recent transposition was observed. Except for Tmt2, the other clades tend to aggregate, and their mode of transposition excluded the master copy model. This suggests that each new copy has the same probability of transposing as other copies. This study provides a better view of the diversity and dynamic nature of gypsy retrotransposons in T. melanosporum. Even if the major gypsy retrotransposon bursts are old, some elements seem to have transposed recently, suggesting that they may continue to model the truffle genomes. PMID:27025914

  17. Age-associated de-repression of retrotransposons in the Drosophila fat body, its potential cause and consequence.

    PubMed

    Chen, Haiyang; Zheng, Xiaobin; Xiao, Danqing; Zheng, Yixian

    2016-06-01

    Eukaryotic genomes contain transposable elements (TE) that can move into new locations upon activation. Since uncontrolled transposition of TEs, including the retrotransposons and DNA transposons, can lead to DNA breaks and genomic instability, multiple mechanisms, including heterochromatin-mediated repression, have evolved to repress TE activation. Studies in model organisms have shown that TEs become activated upon aging as a result of age-associated deregulation of heterochromatin. Considering that different organisms or cell types may undergo distinct heterochromatin changes upon aging, it is important to identify pathways that lead to TE activation in specific tissues and cell types. Through deep sequencing of isolated RNAs, we report an increased expression of many retrotransposons in the old Drosophila fat body, an organ equivalent to the mammalian liver and adipose tissue. This de-repression correlates with an increased number of DNA damage foci and decreased level of Drosophila lamin-B in the old fat body cells. Depletion of the Drosophila lamin-B in the young or larval fat body results in a reduction of heterochromatin and a corresponding increase in retrotransposon expression and DNA damage. Further manipulations of lamin-B and retrotransposon expression suggest a role of the nuclear lamina in maintaining the genome integrity of the Drosophila fat body by repressing retrotransposons. PMID:27072046

  18. Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3

    PubMed Central

    Pachulska-Wieczorek, Katarzyna; Le Grice, Stuart F.J.; Purzycka, Katarzyna J.

    2016-01-01

    Long-terminal repeat (LTR) retrotransposons are transposable genetic elements that replicate intracellularly, and can be considered progenitors of retroviruses. Ty1 and Ty3 are the most extensively characterized LTR retrotransposons whose RNA genomes provide the template for both protein translation and genomic RNA that is packaged into virus-like particles (VLPs) and reverse transcribed. Genomic RNAs are not divided into separate pools of translated and packaged RNAs, therefore their trafficking and packaging into VLPs requires an equilibrium between competing events. In this review, we focus on Ty1 and Ty3 genomic RNA trafficking and packaging as essential steps of retrotransposon propagation. We summarize the existing knowledge on genomic RNA sequences and structures essential to these processes, the role of Gag proteins in repression of genomic RNA translation, delivery to VLP assembly sites, and encapsidation. PMID:27428991

  19. Retrotransposon derepression leads to activation of the unfolded protein response and apoptosis in pro-B cells.

    PubMed

    Pasquarella, Alessandra; Ebert, Anja; Pereira de Almeida, Gustavo; Hinterberger, Maria; Kazerani, Maryam; Nuber, Alexander; Ellwart, Joachim; Klein, Ludger; Busslinger, Meinrad; Schotta, Gunnar

    2016-05-15

    The H3K9me3-specific histone methyltransferase Setdb1 impacts on transcriptional regulation by repressing both developmental genes and retrotransposons. How impaired retrotransposon silencing may lead to developmental phenotypes is currently unclear. Here, we show that loss of Setdb1 in pro-B cells completely abrogates B cell development. In pro-B cells, Setdb1 is dispensable for silencing of lineage-inappropriate developmental genes. Instead, we detect strong derepression of endogenous murine leukemia virus (MLV) copies. This activation coincides with an unusual change in chromatin structure, with only partial loss of H3K9me3 and unchanged DNA methylation, but strongly increased H3K4me3. Production of MLV proteins leads to activation of the unfolded protein response pathway and apoptosis. Thus, our data demonstrate that B cell development depends on the proper repression of retrotransposon sequences through Setdb1. PMID:27013243

  20. Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3.

    PubMed

    Pachulska-Wieczorek, Katarzyna; Le Grice, Stuart F J; Purzycka, Katarzyna J

    2016-01-01

    Long-terminal repeat (LTR) retrotransposons are transposable genetic elements that replicate intracellularly, and can be considered progenitors of retroviruses. Ty1 and Ty3 are the most extensively characterized LTR retrotransposons whose RNA genomes provide the template for both protein translation and genomic RNA that is packaged into virus-like particles (VLPs) and reverse transcribed. Genomic RNAs are not divided into separate pools of translated and packaged RNAs, therefore their trafficking and packaging into VLPs requires an equilibrium between competing events. In this review, we focus on Ty1 and Ty3 genomic RNA trafficking and packaging as essential steps of retrotransposon propagation. We summarize the existing knowledge on genomic RNA sequences and structures essential to these processes, the role of Gag proteins in repression of genomic RNA translation, delivery to VLP assembly sites, and encapsidation. PMID:27428991

  1. Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni

    PubMed Central

    DeMarco, Ricardo; Kowaltowski, Andre T.; Machado, Abimael A.; Soares, M. Bento; Gargioni, Cybele; Kawano, Toshie; Rodrigues, Vanderlei; Madeira, Alda M. B. N.; Wilson, R. Alan; Menck, Carlos F. M.; Setubal, João C.; Dias-Neto, Emmanuel; Leite, Luciana C. C.; Verjovski-Almeida, Sergio

    2004-01-01

    Using the data set of 180,000 expressed sequence tags (ESTs) of the blood fluke Schistosoma mansoni generated recently by our group, we identified three novel long-terminal-repeat (LTR)- and one novel non-LTR-expressed retrotransposon, named Saci-1, -2, and -3 and Perere, respectively. Full-length sequences were reconstructed from ESTs and have deduced open reading frames (ORFs) with several uncorrupted features, characterizing them as possible active retrotransposons of different known transposon families. Alignment of reconstructed sequences to available preliminary genome sequence data confirmed the overall structure of the transposons. The frequency of sequenced transposon transcripts in cercariae was 14% of all transcripts from that stage, twofold higher than that in schistosomula and three- to fourfold higher than that in adults, eggs, miracidia, and germ balls. We show by Southern blot analysis, by EST annotation and tallying, and by counting transposon tags from a Social Analysis of Gene Expression library, that the four novel retrotransposons exhibit a 10- to 30-fold lower copy number in the genome and a 4- to 200-fold-higher transcriptional rate per copy than the four previously described S. mansoni retrotransposons. Such differences lead us to hypothesize that there are two different populations of retrotransposons in S. mansoni genome, occupying different niches in its ecology. Examples of retrotransposon fragment inserts were found into the 5′ and 3′ untranslated regions of four different S. mansoni target gene transcripts. The data presented here suggest a role for these elements in the dynamics of this complex human parasite genome. PMID:14990715

  2. Ylli, a non-LTR retrotransposon L1 family in the dimorphic yeast Yarrowia lipolytica.

    PubMed

    Casaregola, Serge; Neuvéglise, Cécile; Bon, Elisabeth; Gaillardin, Claude

    2002-05-01

    During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side of this zone of homology allowed the definition of an element over 6 kb long. The conceptual translation of this sequence revealed two open reading frames (ORFs) that displayed several characteristics of non-LTR retrotransposons: a Cys-rich motif in the ORF1, an N-terminal endonuclease, a central RT, and a C-terminal zinc finger domain in the ORF2. We called this element Ylli (for Y. lipolytica LINE). A total of 19 distinct repeats carrying the 3' untranslated region (UTR) and all ending with a poly-A tail were detected. Most of them were very short, 17 being 134 bp long or less. The number of copies of Ylli was estimated to be around 100 if these short repeats are 5' truncations. No 5' UTR was clearly identified, indicating that entire and therefore active elements might be very rare in the Y. lipolytica strain tested. Ylli does not seem to have any insertion specificity. Phylogenetic analysis of the RT domain unambiguously placed Ylli within the L1 clade. It forms a monophyletic group with the Zorro non-LTR retrotransposons discovered in another dimorphic yeast Candida albicans. BLAST comparisons showed that ORF2 of Ylli is closely related to that of the slime mold Dictyostelium discoideum L1 family, TRE. PMID:11961100

  3. Retrotransposons at Drosophila telomeres: host domestication of a selfish element for the maintenance of genome integrity

    PubMed Central

    Zhang, Liang; Rong, Yikang S.

    2012-01-01

    Telomere serves two essential functions for the cell. It prevents the recognition of natural chromosome ends as DNA breaks (the end capping function). It counteracts incomplete end replication by adding DNA to the ends of chromosomes (the end elongation function). In most organisms studied, telomerase fulfills the end elongation function. In Drosophila, however, telomere specific retrotransposons have been coerced into performing this essential function for the host. In this review, we focus our discussion on transposition mechanisms and transcriptional regulation of these transposable elements, and present provocative models for the purpose of spurring new interests in the field. PMID:22342531

  4. Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles.

    PubMed

    Palmer, K J; Tichelaar, W; Myers, N; Burns, N R; Butcher, S J; Kingsman, A J; Fuller, S D; Saibil, H R

    1997-09-01

    The virus-like particles (VLPs) produced by the yeast retrotransposon Ty1 are functionally related to retroviral cores. These particles are unusual in that they have variable radif. A paired mass-radius analysis of VLPs by scanning transmission electron microscopy showed that many of these particles form an icosahedral T-number series. Three-dimensional reconstruction to 38-A resolution from cryo-electron micrographs of T = 3 and T = 4 shells revealed that the single structural protein encoded by the TYA gene assembles into spiky shells from trimeric units. PMID:9261411

  5. Disentangling the Relationship of the Australian Marsupial Orders Using Retrotransposon and Evolutionary Network Analyses

    PubMed Central

    Gallus, Susanne; Janke, Axel; Kumar, Vikas; Nilsson, Maria A.

    2015-01-01

    The ancestors to the Australian marsupials entered Australia around 60 (54–72) Ma from Antarctica, and radiated into the four living orders Peramelemorphia, Dasyuromorphia, Diprotodontia, and Notoryctemorphia. The relationship between the four Australian marsupial orders has been a long-standing question, because different phylogenetic studies have not been able to consistently reconstruct the same topology. Initial in silico analysis of the Tasmanian devil genome and experimental screening in the seven marsupial orders revealed 20 informative transposable element insertions for resolving the inter- and intraordinal relationships of Australian and South American orders. However, the retrotransposon insertions support three conflicting topologies regarding Peramelemorphia, Dasyuromorphia, and Notoryctemorphia, indicating that the split between the three orders may be best understood as a network. This finding is supported by a phylogenetic reanalysis of nuclear gene sequences, using a consensus network approach that allows depicting hidden phylogenetic conflict, otherwise lost when forcing the data into a bifurcating tree. The consensus network analysis agrees with the transposable element analysis in that all possible topologies regarding Peramelemorphia, Dasyuromorphia, and Notoryctemorphia in a rooted four-taxon topology are equally well supported. In addition, retrotransposon insertion data support the South American order Didelphimorphia being the sistergroup to all other living marsupial orders. The four Australian orders originated within 3 Myr at the Cretaceous–Paleogene boundary. The rapid divergences left conflicting phylogenetic information in the genome possibly generated by incomplete lineage sorting or introgressive hybridization, leaving the relationship among Australian marsupial orders unresolvable as a bifurcating process millions of years later. PMID:25786431

  6. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes

    PubMed Central

    Kaake, Robyn; Dawson, Anthony R.; Matheos, Dina; Nagashima, Kunio; Sitlani, Parth; Patterson, Kurt; Chang, Ivan; Huang, Lan; Sandmeyer, Suzanne

    2015-01-01

    Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5’ to 3’ exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs. PMID:26421679

  7. Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome.

    PubMed Central

    Friesen, P D; Nissen, M S

    1990-01-01

    A single copy of the retrotransposon TED, from the moth Trichoplusia ni (a lepidopteran noctuid), was identified within the DNA genome of the baculovirus Autographa californica nuclear polyhedrosis virus. Determination of the complete nucleotide sequence (7,510 base pairs) of the integrated copy indicated that TED belongs to the family of retrotransposons that includes Drosophila melanogaster elements 17.6 and gypsy and thus represents the first nondipteran member of this invertebrate group to be identified. The internal portion of TED, flanked by long terminal repeats (LTRs), is composed of three long open reading frames comparable in size and location to the gag, pol, and env genes of the vertebrate retroviruses. Sequence similarity with the dipteran elements was the highest within individual domains of TED open reading frame 2 (pol region) that are also conserved among the retroviruses and encode protease, reverse transcriptase, and integrase functions, respectively. Mapping the 5' and 3' termini of TED RNAs indicated that the LTRs have a retroviral U3-R-U5 structural organization that is capable of directing the synthesis of transcripts that represent potential substrates for reverse transcription and intermediates in transposition. Abundant RNAs were also initiated from a site within the 5' LTR that matches the consensus motif for the promoter of late, hyperexpressed baculovirus genes. The presence of this viruslike promoter within TED and its subsequent activation only after integration within the viral genome suggest a possible symbiotic relationship with the baculovirus that could extend transposon host range. Images PMID:1692964

  8. Co-evolution of plant LTR-retrotransposons and their host genomes.

    PubMed

    Zhao, Meixia; Ma, Jianxin

    2013-07-01

    Transposable elements (TEs), particularly, long terminal repeat retrotransposons (LTR-RTs), are the most abundant DNA components in all plant species that have been investigated, and are largely responsible for plant genome size variation. Although plant genomes have experienced periodic proliferation and/or recent burst of LTR-retrotransposons, the majority of LTR-RTs are inactivated by DNA methylation and small RNA-mediated silencing mechanisms, and/or were deleted/truncated by unequal homologous recombination and illegitimate recombination, as suppression mechanisms that counteract genome expansion caused by LTR-RT amplification. LTR-RT DNA is generally enriched in pericentromeric regions of the host genomes, which appears to be the outcomes of preferential insertions of LTR-RTs in these regions and low effectiveness of selection that purges LTR-RT DNA from these regions relative to chromosomal arms. Potential functions of various TEs in their host genomes remain blurry; nevertheless, LTR-RTs have been recognized to play important roles in maintaining chromatin structures and centromere functions and regulation of gene expressions in their host genomes. PMID:23794032

  9. rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus

    PubMed Central

    Shpiz, Sergey; Kwon, Dmitry; Rozovsky, Yakov; Kalmykova, Alla

    2009-01-01

    Telomeres in Drosophila are maintained by the specialized telomeric retrotransposons HeT-A, TART and TAHRE. Sense transcripts of telomeric retroelements were shown to be the targets of a specialized RNA-interference mechanism, a repeat-associated short interfering (rasi)RNA-mediated system. Antisense rasiRNAs play a key role in this mechanism, highlighting the importance of antisense expression in retrotransposon silencing. Previously, bidirectional transcription was reported for the telomeric element TART. Here, we show that HeT-A is also bidirectionally transcribed, and HeT-A antisense transcription in ovaries is regulated by a promoter localized within its 3′ untranslated region. A remarkable feature of noncoding HeT-A antisense transcripts is the presence of multiple introns. We demonstrate that sense and antisense HeT-A-specific rasiRNAs are present in the same tissue, indicating that transcripts of both directions may be considered as natural targets of the rasiRNA pathway. We found that the expression of antisense transcripts of telomeric elements is regulated by the RNA silencing machinery, suggesting rasiRNA-mediated interplay between sense and antisense transcripts in the cell. Finally, this regulation occurs in the nucleus since disruption of the rasiRNA pathway leads to an accumulation of TART and HeT-A transcripts in germ cell nuclei. PMID:19036789

  10. Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses.

    PubMed

    Gallus, Susanne; Janke, Axel; Kumar, Vikas; Nilsson, Maria A

    2015-04-01

    The ancestors to the Australian marsupials entered Australia around 60 (54-72) Ma from Antarctica, and radiated into the four living orders Peramelemorphia, Dasyuromorphia, Diprotodontia, and Notoryctemorphia. The relationship between the four Australian marsupial orders has been a long-standing question, because different phylogenetic studies have not been able to consistently reconstruct the same topology. Initial in silico analysis of the Tasmanian devil genome and experimental screening in the seven marsupial orders revealed 20 informative transposable element insertions for resolving the inter- and intraordinal relationships of Australian and South American orders. However, the retrotransposon insertions support three conflicting topologies regarding Peramelemorphia, Dasyuromorphia, and Notoryctemorphia, indicating that the split between the three orders may be best understood as a network. This finding is supported by a phylogenetic reanalysis of nuclear gene sequences, using a consensus network approach that allows depicting hidden phylogenetic conflict, otherwise lost when forcing the data into a bifurcating tree. The consensus network analysis agrees with the transposable element analysis in that all possible topologies regarding Peramelemorphia, Dasyuromorphia, and Notoryctemorphia in a rooted four-taxon topology are equally well supported. In addition, retrotransposon insertion data support the South American order Didelphimorphia being the sistergroup to all other living marsupial orders. The four Australian orders originated within 3 Myr at the Cretaceous-Paleogene boundary. The rapid divergences left conflicting phylogenetic information in the genome possibly generated by incomplete lineage sorting or introgressive hybridization, leaving the relationship among Australian marsupial orders unresolvable as a bifurcating process millions of years later. PMID:25786431

  11. Primate-specific ORF0 contributes to retrotransposon-mediated diversity.

    PubMed

    Denli, Ahmet M; Narvaiza, Iñigo; Kerman, Bilal E; Pena, Monique; Benner, Christopher; Marchetto, Maria C N; Diedrich, Jolene K; Aslanian, Aaron; Ma, Jiao; Moresco, James J; Moore, Lynne; Hunter, Tony; Saghatelian, Alan; Gage, Fred H

    2015-10-22

    LINE-1 retrotransposons are fast-evolving mobile genetic entities that play roles in gene regulation, pathological conditions, and evolution. Here, we show that the primate LINE-1 5'UTR contains a primate-specific open reading frame (ORF) in the antisense orientation that we named ORF0. The gene product of this ORF localizes to promyelocytic leukemia-adjacent nuclear bodies. ORF0 is present in more than 3,000 loci across human and chimpanzee genomes and has a promoter and a conserved strong Kozak sequence that supports translation. By virtue of containing two splice donor sites, ORF0 can also form fusion proteins with proximal exons. ORF0 transcripts are readily detected in induced pluripotent stem (iPS) cells from both primate species. Capped and polyadenylated ORF0 mRNAs are present in the cytoplasm, and endogenous ORF0 peptides are identified upon proteomic analysis. Finally, ORF0 enhances LINE-1 mobility. Taken together, these results suggest a role for ORF0 in retrotransposon-mediated diversity. PMID:26496605

  12. Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome.

    PubMed

    Kubat, Zdenek; Zluvova, Jitka; Vogel, Ivan; Kovacova, Viera; Cermak, Tomas; Cegan, Radim; Hobza, Roman; Vyskot, Boris; Kejnovsky, Eduard

    2014-04-01

    Some transposable elements (TEs) show extraordinary variance in abundance along sex chromosomes but the mechanisms responsible for this variance are unknown. Here, we studied Ogre long terminal repeat (LTR) retrotransposons in Silene latifolia, a dioecious plant with evolutionarily young heteromorphic sex chromosomes. Ogre elements are ubiquitous in the S. latifolia genome but surprisingly absent on the Y chromosome. Bacterial artificial chromosome (BAC) library analysis and fluorescence in situ hybridization (FISH) were used to determine Ogre structure and chromosomal localization. Next generation sequencing (NGS) data were analysed to assess the transcription level and abundance of small RNAs. Methylation of Ogres was determined by bisulphite sequencing. Phylogenetic analysis was used to determine mobilization time and selection forces acting on Ogre elements. We characterized three Ogre families ubiquitous in the S. latifolia genome. One family is nearly absent on the Y chromosome despite all the families having similar structures and spreading mechanisms. We showed that Ogre retrotransposons evolved before sex chromosomes appeared but were mobilized after formation of the Y chromosome. Our data suggest that the absence of one Ogre family on the Y chromosome may be caused by 24-nucleotide (24-nt) small RNA-mediated silencing leading to female-specific spreading. Our findings highlight epigenetic silencing mechanisms as potentially crucial factors in sex-specific spreading of some TEs, but other possible mechanisms are also discussed. PMID:24456522

  13. Retrotransposon-Induced Heterochromatin Spreading in the Mouse Revealed by Insertional Polymorphisms

    PubMed Central

    Rebollo, Rita; Karimi, Mohammad M.; Bilenky, Misha; Gagnier, Liane; Miceli-Royer, Katharine; Zhang, Ying; Goyal, Preeti; Keane, Thomas M.; Jones, Steven; Hirst, Martin; Lorincz, Matthew C.; Mager, Dixie L.

    2011-01-01

    The “arms race” relationship between transposable elements (TEs) and their host has promoted a series of epigenetic silencing mechanisms directed against TEs. Retrotransposons, a class of TEs, are often located in repressed regions and are thought to induce heterochromatin formation and spreading. However, direct evidence for TE–induced local heterochromatin in mammals is surprisingly scarce. To examine this phenomenon, we chose two mouse embryonic stem (ES) cell lines that possess insertionally polymorphic retrotransposons (IAP, ETn/MusD, and LINE elements) at specific loci in one cell line but not the other. Employing ChIP-seq data for these cell lines, we show that IAP elements robustly induce H3K9me3 and H4K20me3 marks in flanking genomic DNA. In contrast, such heterochromatin is not induced by LINE copies and only by a minority of polymorphic ETn/MusD copies. DNA methylation is independent of the presence of IAP copies, since it is present in flanking regions of both full and empty sites. Finally, such spreading into genes appears to be rare, since the transcriptional start sites of very few genes are less than one Kb from an IAP. However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness. PMID:21980304

  14. Retrotransposon-associated long non-coding RNAs in mice and men.

    PubMed

    Ganesh, Sravya; Svoboda, Petr

    2016-06-01

    Over a half of mammalian genomes is occupied by repetitive elements whose ability to provide functional sequences, move into new locations, and recombine underlies the so-called genome plasticity. At the same time, mobile elements exemplify selfish DNA, which is expanding in the genome at the expense of the host. The selfish generosity of mobile genetic elements is in the center of research interest as it offers insights into mechanisms underlying evolution and emergence of new genes. In terms of numbers, with over 20,000 in count, protein-coding genes make an outstanding >2 % minority. This number is exceeded by an ever-growing list of genes producing long non-coding RNAs (lncRNAs), which do not encode for proteins. LncRNAs are a dynamically evolving population of genes. While it is not yet clear what fraction of lncRNAs represents functionally important ones, their features imply that many lncRNAs emerge at random as new non-functional elements whose functionality is acquired through natural selection. Here, we explore the intersection of worlds of mobile genetic elements (particularly retrotransposons) and lncRNAs. In addition to summarizing essential features of mobile elements and lncRNAs, we focus on how retrotransposons contribute to lncRNA evolution, structure, and function in mammals. PMID:27044413

  15. Determining and dating recent rodent speciation events by using L1 (LINE-1) retrotransposons

    PubMed Central

    Verneau, Olivier; Catzeflis, François; Furano, Anthony V.

    1998-01-01

    Phylogenies based on the inheritance of shared derived characters will be ambiguous when the shared characters are not the result of common ancestry. Such characters are called homoplasies. Phylogenetic analysis also can be problematic if the characters have not changed sufficiently, as might be the case for rapid or recent speciations. The latter are of particular interest because evolutionary processes may be more accessible the more recent the speciation. The repeated DNA subfamilies generated by the mammalian L1 (LINE-1) retrotransposon are apparently homoplasy-free phylogenetic characters. L1 retrotransposons are transmitted only by inheritance and rapidly generate novel variants that produce distinct subfamilies of mostly defective copies, which then “age” as they diverge. Here we show that the L1 character can both resolve and date recent speciation events within the large group of very closely related rats known as Rattus sensu stricto. This lineage arose 5–6 million years ago (Mya) and subsequently underwent two episodes of speciation: an intense one, ≈2.7 Mya, produced at least five lineages in <0.3 My; a second began ≈1.2 Mya and may still be continuing. PMID:9736728

  16. Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor

    PubMed Central

    Morales-Hernández, Antonio; González-Rico, Francisco J.; Román, Angel C.; Rico-Leo, Eva; Alvarez-Barrientos, Alberto; Sánchez, Laura; Macia, Ángela; Heras, Sara R.; García-Pérez, José L.; Merino, Jaime M.; Fernández-Salguero, Pedro M.

    2016-01-01

    Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, their role in gene regulation is poorly understood. Here, we show that the dioxin receptor (AHR) leads to differentiation of human carcinoma cells through the transcriptional upregulation of Alu retrotransposons, whose RNA transcripts can repress pluripotency genes. Despite the genome-wide presence of Alu elements, we provide evidences that those located at the NANOG and OCT4 promoters bind AHR, are transcribed by RNA polymerase-III and repress NANOG and OCT4 in differentiated cells. OCT4 and NANOG repression likely involves processing of Alu-derived transcripts through the miRNA machinery involving the Microprocessor and RISC. Consistently, stable AHR knockdown led to basal undifferentiation, impaired Alus transcription and blockade of OCT4 and NANOG repression. We suggest that transcripts produced from AHR-regulated Alu retrotransposons may control the expression of stemness genes OCT4 and NANOG during differentiation of carcinoma cells. The control of discrete Alu elements by specific transcription factors may have a dynamic role in genome regulation under physiological and diseased conditions. PMID:26883630

  17. Mutant gene phenotypes mediated by a Drosophila melanogaster retrotransposon require sequences homologous to mammalian enhancers.

    PubMed Central

    Geyer, P K; Green, M M; Corces, V G

    1988-01-01

    We have analyzed the molecular structure of phenotypic revertants of gypsy-induced mutations to understand the molecular mechanisms by which this retrotransposon causes mutant phenotypes in Drosophila melanogaster. The independent partial revertants analyzed are caused by the insertion of different transposons into the same region of gypsy. One partial revertant of the yellow allele y2 arose as a consequence of the insertion of the jockey mobile element into gypsy sequences, whereas a second incomplete revertant is due to the insertion of the hobo transposon. In addition, a previously isolated partial revertant of the Hairy-wing allele Hw1 resulted from the integration of the BS transposable element into the same gypsy sequences. The region affected by the insertion of the three transposons contains 12 copies of a repeated motif that shows striking homology to mammalian transcriptional enhancers. Our results suggest that these sequences, which might be involved in the transcriptional control of the gypsy element, are also responsible for the induction of mutant phenotypes by this retrotransposon. PMID:2847167

  18. Characterization of retrotransposon sequences expressed in inflorescences of apomictic and sexual Paspalum notatum plants.

    PubMed

    Ochogavía, Ana Claudia; Seijo, José Guillermo; González, Ana María; Podio, Maricel; Duarte Silveira, Erica; Machado Lacerda, Ana Luiza; Tavares de Campos Carneiro, Vera; Ortiz, Juan Pablo A; Pessino, Silvina Claudia

    2011-09-01

    Apomixis, an asexual mode of reproduction through seeds, holds much promise for agricultural advances. However, the molecular mechanisms underlying this trait are still poorly understood. We previously isolated several transcripts representing novel sequences differentially expressed in reproductive tissues of sexual and apomictic plants. Here, we report the characterization of two of these unknown RNA transcripts (experimental codes N17 and N22). Since original fragments showed no significant homologies to sequences at databases, preliminary genomic PCR experiments were carried out to discard possible contaminations. RACE extension on flanking regions provided longer sequences for the candidates and additional related transcripts, which revealed similarity to LTR retrotransposons carrying short transduplicated segments of protein-coding genes. Interestingly, some transduplicated segments corresponded to genes previously associated with apomictic development. Gene copy number estimations revealed a moderate representation of the elements in the genome, with significantly increased numbers in a sexual genotype with respect to an apomictic one. Genetic mapping of N17 showed that a copy of this particular element was located onto Paspalum notatum linkage group F3c, at a central non-recombinant region resembling a centromere. Expression analysis showed an increased activity of N17 and N22 sense strands in ovules of the sexual genotypes. A retrotransposon-specific differential display analysis aimed at detecting related sequences allowed the identification of a complex family, with the majority of its members represented in the sexual genotype. Our results suggest that these elements could be participating in regulatory pathways related to apomixis and sexuality. PMID:21394488

  19. LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots

    PubMed Central

    Zhu, Zhenglin; Tan, Shengjun; Zhang, Yaqiong; Zhang, Yong E.

    2016-01-01

    RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotransposons appear to be the major player in plants, although an L1-like mechanism has also been hypothesized to be involved in retroposition. We tested this hypothesis by searching for young retrocopies, as these still retain the sequence features associated with the underlying retroposition mechanism. Specifically, we identified polymorphic retrocopies (retroCNVs) by analyzing public Arabidopsis (Arabidopsis thaliana) resequencing data. Furthermore, we searched for recently originated retrocopies encoded by the reference genome of Arabidopsis and Manihot esculenta. Across these two datasets, we found cases with L1-like hallmarks, namely, the expected target site sequence, a polyA tail and target site duplications. Such data suggest that an L1-like mechanism could operate in plants, especially dicots. PMID:27098918

  20. Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor.

    PubMed

    Morales-Hernández, Antonio; González-Rico, Francisco J; Román, Angel C; Rico-Leo, Eva; Alvarez-Barrientos, Alberto; Sánchez, Laura; Macia, Ángela; Heras, Sara R; García-Pérez, José L; Merino, Jaime M; Fernández-Salguero, Pedro M

    2016-06-01

    Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, their role in gene regulation is poorly understood. Here, we show that the dioxin receptor (AHR) leads to differentiation of human carcinoma cells through the transcriptional upregulation of Alu retrotransposons, whose RNA transcripts can repress pluripotency genes. Despite the genome-wide presence of Alu elements, we provide evidences that those located at the NANOG and OCT4 promoters bind AHR, are transcribed by RNA polymerase-III and repress NANOG and OCT4 in differentiated cells. OCT4 and NANOG repression likely involves processing of Alu-derived transcripts through the miRNA machinery involving the Microprocessor and RISC. Consistently, stable AHR knockdown led to basal undifferentiation, impaired Alus transcription and blockade of OCT4 and NANOG repression. We suggest that transcripts produced from AHR-regulated Alu retrotransposons may control the expression of stemness genes OCT4 and NANOG during differentiation of carcinoma cells. The control of discrete Alu elements by specific transcription factors may have a dynamic role in genome regulation under physiological and diseased conditions. PMID:26883630

  1. Splicing of Retrotransposon Insertions from Transcripts of the Drosophila Melanogaster Vermilion Gene in a Revertant

    PubMed Central

    Pret, A. M.; Searles, L. L.

    1991-01-01

    A mutation of the Drosophila melanogaster vermilion (v) gene known as v(1) is caused by the insertion of a 412 retrotransposon into the 5' untranslated region of the first exon. Mutants carrying this insertion accumulate a low level of mRNA from which most of the transposon sequences have been eliminated by splicing at cryptic sites within transposon sequences. Here, we demonstrate that a revertant of the v(1) allele called v(+37) is caused by the insertion of a second retrotransposon, the B104/roo element, into a site near one end of the 412 element. The revertant strain accumulates a higher level of mRNA from which most of both transposons have been removed by splicing at new donor sites introduced by the B104/roo insertion and the same acceptor site within 412. Mutations at suppressor of sable [su(s)], which increase the accumulation of v(1) transcripts, slightly elevate the level of v(+37) RNA. In addition, we show that the first v intron downstream of the 412 insertion is not efficiently removed in the v(1) mutant, and suppressor and reversion mutations increase the proportion of transcripts that are properly spliced at that downstream intron. Thus, it appears that both the suppressor and reversion mutations exert an effect at the level of pre-mRNA splicing. PMID:1664404

  2. LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots.

    PubMed

    Zhu, Zhenglin; Tan, Shengjun; Zhang, Yaqiong; Zhang, Yong E

    2016-01-01

    RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotransposons appear to be the major player in plants, although an L1-like mechanism has also been hypothesized to be involved in retroposition. We tested this hypothesis by searching for young retrocopies, as these still retain the sequence features associated with the underlying retroposition mechanism. Specifically, we identified polymorphic retrocopies (retroCNVs) by analyzing public Arabidopsis (Arabidopsis thaliana) resequencing data. Furthermore, we searched for recently originated retrocopies encoded by the reference genome of Arabidopsis and Manihot esculenta. Across these two datasets, we found cases with L1-like hallmarks, namely, the expected target site sequence, a polyA tail and target site duplications. Such data suggest that an L1-like mechanism could operate in plants, especially dicots. PMID:27098918

  3. Transcriptome Analysis of ESTs from a Chaetognath Reveals a Deep-Branching Clade of Retrovirus-Like Retrotransposons.

    PubMed

    Barthélémy, Roxane M; Casanova, Jean-Paul; Faure, Eric

    2008-01-01

    Chaetognaths constitute a small marine phylum exhibiting several characteristic which are highly unusual in animal genomes, including two classes of both rRNA and protein ribosomal genes. As in this phylum presence of retrovirus-like elements has never been documented, analysis of a published expressed sequence tag (EST) collection of the chaetognath Spadella cephaloptera has been made. Twelve sequences representing transcript sections of reverse transcriptase domain of active retrotransposons were isolated from~11,000 ESTs. Five of them are originated from Gypsy retrovirus-like elements, whereas the other are transcripts from a Bel-Pao LTR-retrotransposon, a Penelope-like element and LINE retrotransposons. Moreover, a part of a putative integrase has also been found. Phylogenetic analyses suggest a deep-branching clade of the retrovirus-like elements, which is in agreement with the probably Cambrian origin of the phylum. Moreover, retrotransposons have not been found in telomeric-like transcripts which are probably constituted by both vertebrate and arthropod canonical repeats. PMID:19440464

  4. Exploiting the power of LINE-1 retrotransposon mutagenesis for identification of genes involved in embryonic stem cell differentiation.

    PubMed

    Lenka, Nibedita; Krishnan, Shruthi; Board, Philip; Rangasamy, Danny

    2014-06-01

    Identifying the genes or epigenetic factors that control the self-renewal and differentiation of stem cells is critical to understanding the molecular basis of cell commitment. Although a number of insertional mutagenesis vectors have been developed for identifying gene functions in animal models, the L1 retrotransposition system offers additional advantages as a tool to disrupt genes in embryonic stem cells in order to identify their functions and the phenotypes associated with them. Recent advances in producing synthetic versions of L1 retrotransposon vector system and the optimization of techniques to accurately identify retrotransposon integration sites have increased their utility for gene discovery applications. We have developed a novel episomal, nonviral L1 retrotransposon vector using scaffold/matrix attachment regions that provides stable, sustained levels of retrotransposition in cell cultures without being affected by epigenetic silencing or from some of the common problems of vector integration. This modified vector contains a GFP marker whose expression occurs only after successful gene disruption events and thus the cells with disrupted genes can be easily picked for functional analysis. Here we present a method to disrupt gene function in embryonic stem cells that aid in the identification of genes involved in stem cell differentiation processes. The methods presented here can be easily adapted to the study of other types of cancer stem cells or induced pluripotent stem cells using the L1 retrotransposon as an insertional mutagen. PMID:24610122

  5. Transcriptome Analysis of ESTs from a Chaetognath Reveals a Deep-Branching Clade of Retrovirus-Like Retrotransposons

    PubMed Central

    Barthélémy, Roxane M; Casanova, Jean-Paul; Faure, Eric

    2008-01-01

    Chaetognaths constitute a small marine phylum exhibiting several characteristic which are highly unusual in animal genomes, including two classes of both rRNA and protein ribosomal genes. As in this phylum presence of retrovirus-like elements has never been documented, analysis of a published expressed sequence tag (EST) collection of the chaetognath Spadella cephaloptera has been made. Twelve sequences representing transcript sections of reverse transcriptase domain of active retrotransposons were isolated from~11,000 ESTs. Five of them are originated from Gypsy retrovirus-like elements, whereas the other are transcripts from a Bel-Pao LTR-retrotransposon, a Penelope-like element and LINE retrotransposons. Moreover, a part of a putative integrase has also been found. Phylogenetic analyses suggest a deep-branching clade of the retrovirus-like elements, which is in agreement with the probably Cambrian origin of the phylum. Moreover, retrotransposons have not been found in telomeric-like transcripts which are probably constituted by both vertebrate and arthropod canonical repeats. PMID:19440464

  6. Recent Expansion of a New Ingi-Related Clade of Vingi non-LTR Retrotransposons in Hedgehogs

    PubMed Central

    Kojima, Kenji K.; Kapitonov, Vladimir V.; Jurka, Jerzy

    2011-01-01

    Autonomous non-long terminal repeat (non-LTR) retrotransposons and their repetitive remnants are ubiquitous components of mammalian genomes. Recently, we identified non-LTR retrotransposon families, Ingi-1_AAl and Ingi-1_EE, in two hedgehog genomes. Here we rename them to Vingi-1_AAl and Vingi-1_EE and report a new clade “Vingi,” which is a sister clade of Ingi that lacks the ribonuclease H domain. In the European hedgehog genome, there are 11 non-autonomous families of elements derived from Vingi-1_EE by internal deletions. No retrotransposons related to Vingi elements were found in any of the remaining 33 mammalian genomes nearly completely sequenced to date, but we identified several new families of Vingi and Ingi retrotransposons outside mammals. Our data suggest the horizontal transfer of Vingi elements to hedgehog, although the vertical transfer cannot be ruled out. The compact structure and trans-mobilization of nonautonomous derivatives of Vingi can make them useful for in vivo retrotransposition assay system. PMID:20716533

  7. The insertion of a novel retrotransposon in the promoter of a vernalization gene resulted in early flowering in tetraploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous reports showed allelic variation in wheat vernalization gene VRN1 was due to deletions either in the promoter or the first intron. Here, we identified a novel Vrn-B1 allele that has a retrotransposon in its promoter conferring spring growth habit. The VRN-B1 gene was mapped in a doubled hap...

  8. Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses.

    PubMed

    Santos, Fabíola Carvalho; Guyot, Romain; do Valle, Cacilda Borges; Chiari, Lucimara; Techio, Vânia Helena; Heslop-Harrison, Pat; Vanzela, André Luís Laforga

    2015-09-01

    Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low-copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thousands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequences that amplify via an RNA intermediate and reinsert into the genome, are often the major fraction of a genome. Here, we put research on retrotransposons into the larger context of plant repetitive DNA and genome behaviour, showing features of genome evolution in a grass genus, Brachiaria, in relation to other plant species. We show the contrasting amplification of different retroelement fractions across the genome with characteristics for various families and domains. The genus Brachiaria includes both diploid and polyploid species, with similar chromosome types and chromosome basic numbers x = 6, 7, 8 and 9. The polyploids reproduce asexually and are apomictic, but there are also sexual species. Cytogenetic studies and flow cytometry indicate a large variation in DNA content (C-value), chromosome sizes and genome organization. In order to evaluate the role of transposable elements in the genome and karyotype organization of species of Brachiaria, we searched for sequences similar to conserved regions of TEs in RNAseq reads library produced in Brachiaria decumbens. Of the 9649 TE-like contigs, 4454 corresponded to LTR-retrotransposons, and of these, 79.5 % were similar to members of the gypsy superfamily. Sequences of conserved protein domains of gypsy were used to design primers for producing the probes. The probes were used in FISH against chromosomes of accesses of B. decumbens, Brachiaria brizantha, Brachiaria ruziziensis and Brachiaria humidicola. Probes showed hybridization signals predominantly in proximal regions, especially those for retrotransposons of the clades CRM and Athila, while elements of Del and Tat

  9. The varying microsporidian genome: existence of long-terminal repeat retrotransposon in domesticated silkworm parasite Nosema bombycis.

    PubMed

    Xu, Jinshan; Pan, Guoqing; Fang, Lin; Li, Jun; Tian, Xiangjun; Li, Tian; Zhou, Zeyang; Xiang, Zhonghuai

    2006-08-01

    Microsporidia are a group of intracellular parasites with an extremely compact genome and there is no confirmed evidence that retroelements are parasitised in these organisms. Using the dataset of 200,000 genomic shotgun reads of the silkworm pebrine Nosema bombycis, we have identified the eight complete N. bombycis long-terminal repeat retrotransposon (Nbr) elements. All of the Nbr elements are Ty3/gypsy members and have close relationships to Saccharomycetes long-terminal repeat retrotransposons identified previously, providing further evidence of their relationship to fungi. To explore the effect of retrotransposons in microsporidian genome evolution, their distribution was characterised by comparisons between two N. bombycis contigs containing the Nbr elements with the completed genome of the human parasite Encephalitozoon cuniculi, which is closely related to N. bombycis. The Nbr elements locate between or beside syntenic blocks, which are often clustered with other transposable-like sequences, indicating that they are associated with genome size variation and syntenic discontinuities. The ratios of the number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site of the open reading frames among members of each of the eight Nbr families were estimated, which reveal the purifying selection acted on the N. bombycis long-terminal repeat retrotransposons. These results strongly suggest that retrotransposons play a major role in reorganization of the microsporidian genome and they might be active. The present study presents an initial characterization of some transposable elements in the N. bombycis genome and provides some insight into the evolutionary mechanism of microsporidian genomes. PMID:16797019

  10. Acquisition of Full-Length Viral Helicase Domains by Insect Retrotransposon-Encoded Polypeptides

    PubMed Central

    Lazareva, Ekaterina; Lezzhov, Alexander; Vassetzky, Nikita; Solovyev, Andrey; Morozov, Sergey

    2015-01-01

    Recent metagenomic studies in insects identified many sequences unexpectedly closely related to plant virus genes. Here we describe a new example of this kind, insect R1 LINEs with an additional C-terminal domain in their open reading frame 2. This domain is similar to NTPase/helicase (SF1H) domains, which are found in replicative proteins encoded by plant viruses of the genus Tobamovirus. We hypothesize that the SF1H domain could be acquired by LINEs, directly or indirectly, upon insect feeding on virus-infected plants. Possible functions of this domain in LINE transposition and involvement in LINEs counteraction the silencing-based cell defense against retrotransposons are discussed. PMID:26733982

  11. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

    PubMed Central

    Suh, Alexander; Witt, Christopher C.; Menger, Juliana; Sadanandan, Keren R.; Podsiadlowski, Lars; Gerth, Michael; Weigert, Anne; McGuire, Jimmy A.; Mudge, Joann; Edwards, Scott V.; Rheindt, Frank E.

    2016-01-01

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. PMID:27097561

  12. Ectopic Expression of Retrotransposon-Derived PEG11/RTL1 Contributes to the Callipyge Muscular Hypertrophy

    PubMed Central

    Xu, Xuewen; Ectors, Fabien; Davis, Erica E.; Pirottin, Dimitri; Cheng, Huijun; Farnir, Frédéric; Hadfield, Tracy; Cockett, Noelle; Charlier, Carole; Georges, Michel; Takeda, Haruko

    2015-01-01

    The callipyge phenotype is an ovine muscular hypertrophy characterized by polar overdominance: only heterozygous +Mat/CLPGPat animals receiving the CLPG mutation from their father express the phenotype. +Mat/CLPGPat animals are characterized by postnatal, ectopic expression of Delta-like 1 homologue (DLK1) and Paternally expressed gene 11/Retrotransposon-like 1 (PEG11/RTL1) proteins in skeletal muscle. We showed previously in transgenic mice that ectopic expression of DLK1 alone induces a muscular hypertrophy, hence demonstrating a role for DLK1 in determining the callipyge hypertrophy. We herein describe newly generated transgenic mice that ectopically express PEG11 in skeletal muscle, and show that they also exhibit a muscular hypertrophy phenotype. Our data suggest that both DLK1 and PEG11 act together in causing the muscular hypertrophy of callipyge sheep. PMID:26474044

  13. Nucleotide sequence analysis of a cloned DNA fragment from human cells reveals homology to retrotransposons.

    PubMed Central

    Flügel, R M; Maurer, B; Bannert, H; Rethwilm, A; Schnitzler, P; Darai, G

    1987-01-01

    During molecular cloning of proviral DNA of human spumaretrovirus, various recombinant clones were established and analyzed. Blot hybridization revealed that one of the recombinant plasmids had the characteristic features of a member of the long interspersed repetitive sequences family. The DNA element was analyzed by restriction mapping and nucleotide sequencing. It showed a high degree of amino acid sequence homology of 54.3% when compared with the 5'-terminal part of the pol gene product of the murine retrotransposon LIMd. The 3' region of the cloned DNA element encodes proteins with an even higher degree of homology of 67.4% in comparison to the corresponding parts of a member of the primate KpnI sequence family. Images PMID:3031462

  14. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.

    PubMed

    Suh, Alexander; Witt, Christopher C; Menger, Juliana; Sadanandan, Keren R; Podsiadlowski, Lars; Gerth, Michael; Weigert, Anne; McGuire, Jimmy A; Mudge, Joann; Edwards, Scott V; Rheindt, Frank E

    2016-01-01

    Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83-99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25-22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20-17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. PMID:27097561

  15. An epi [c] genetic battle: LINE-1 retrotransposons and intragenomic conflict in humans.

    PubMed

    Muñoz-Lopez, Martin; Macia, Angela; Garcia-Cañadas, Marta; Badge, Richard M; Garcia-Perez, Jose L

    2011-07-01

    The ongoing activity of the human retrotransposon Long Interspersed Element 1 (LINE-1 or L1) continues to impact the human genome in various ways. Throughout evolution, mammalian and primate genomes have been under selection to generate strategies to reduce the activity of selfish DNA like L1. Similarly, selfish DNA has evolved to elude these containment systems. This intragenomic conflict has left many inactive versions of LINEs and other Transposable Elements (TEs) littering the human genome, which together account for roughly half of our DNA. Here, we survey the distinct mechanisms operating in the human genome that seem to reduce the mobility of L1s. In addition, we discuss recent findings that strongly suggest epigenetic mechanisms specifically regulate L1 activity in pluripotent human cells. PMID:22016860

  16. Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames

    PubMed Central

    Behrens, Ralf; Hayles, Jacky; Nurse, Paul

    2000-01-01

    Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100–420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed. PMID:11095681

  17. Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data.

    PubMed

    Cömertpay, G; Baloch, F S; Derya, M; Andeden, E E; Alsaleh, A; Sürek, H; Özkan, H

    2016-01-01

    Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine inter-primer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon- and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties. PMID:26909982

  18. Comparative Genomic Analysis Reveals Multiple Long Terminal Repeats, Lineage-Specific Amplification, and Frequent Interelement Recombination for Cassandra Retrotransposon in Pear (Pyrus bretschneideri Rehd.)

    PubMed Central

    Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling

    2014-01-01

    Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. PMID:24899073

  19. Expression and Processing of Proteins Encoded by the Saccharomyces Retrotransposon Ty5†

    PubMed Central

    Irwin, Phillip A.; Voytas, Daniel F.

    2001-01-01

    Retroelements (retrotransposons and retroviruses) have two genes in common: gag, which specifies structural proteins that form a virus or virus-like particle, and pol, which specifies catalytic proteins required for replication. For many retroelements, gag and pol are present on separate reading frames. Their expression is highly regulated, and the ratio of Gag to Pol is critical for retroelement replication. The Saccharomyces retrotransposon Ty5 contains a single open reading frame, and we characterized Gag and Pol expression by generating transpositionally active Ty5 elements with epitope tags at the N terminus or C terminus or within the integrase coding region. Immunoblot analysis identified two Gag species (Gag-p27 and Gag-p37), reverse transcriptase (Pol-p59), and integrase (Pol-p80), all of which are largely insoluble in the absence of urea or ionic detergent. These proteins result from proteolytic processing of a polyprotein, because elements with mutations in the presumed active site of Ty5 protease express a single tagged protein (Gag-Pol-p182). Protease mutants are also transpositionally inactive. In a time course experiment, we monitored protein expression, proteolytic processing, and transposition of a Ty5 element with identical epitope tags at its N and C termini. Both transposition and the abundance of Gag-p27 increased over time. In contrast, the levels of Gag-p37 and reverse transcriptase peaked after ∼14 h of induction and then gradually decreased. This may be due to differences in stability of Gag-p27 relative to Gag-p37 and reverse transcriptase. The ratio of Ty5 Gag to Pol averaged 5:1 throughout the time course experiment, suggesting that differential protein stability regulates the amounts of these proteins. PMID:11160677

  20. [Study of the transcriptional and transpositional activities of the Tirant retrotransposon in Drosophila melanogaster strains mutant for the flamenco locus].

    PubMed

    Nefedova, L N; Urusov, F A; Romanova, N I; Shmel'kova, A O; Kim, A I

    2012-11-01

    Transpositions of the gypsy retrotransposon in the Drosophila melanogaster genome are controlled by the flamenco locus, which is represented as an accumulation of defective copies of transposable elements. In the present work, genetic control by the flamenco locus of the transcriptional and transpositional activities of the Tirant retrotransposon from the gypsy group was studied. Tissue-specific expression of Tirant was detected in the tissues of ovaries in a strain mutant for the flamenco locus. Tirant was found to be transpositionally active in isogenic D. melanogaster strains mutant for the flamenco locus. The sites of two new insertions have been localized by the method of subtractive hybridization. It has been concluded from the results obtained that the flamenco locus is involved in the genetic control of Tirant transpositions. PMID:23297482

  1. Jule from the fish Xiphophorus is the first complete vertebrate Ty3/Gypsy retrotransposon from the Mag family.

    PubMed

    Volff, J N; Körting, C; Altschmied, J; Duschl, J; Sweeney, K; Wichert, K; Froschauer, A; Schartl, M

    2001-02-01

    Jule is the second complete long-terminal-repeat (LTR) Ty3/Gypsy retrotransposon identified to date in vertebrates. Jule, first isolated from the poeciliid fish Xiphophorus maculatus, is 4.8 kb in length, is flanked by two 202-bp LTRs, and encodes Gag (structural core protein) and Pol (protease, reverse transcriptase, RNase H, and integrase, in that order) but no envelope. There are three to four copies of Jule per haploid genome in X. maculatus. Two of them are located in a subtelomeric region of the sex chromosomes, where they are associated with the Xmrk receptor tyrosine kinase genes, of which oncogenic versions are responsible for the formation of hereditary melanoma in Xiphophorus. One almost intact copy of Jule was found in the first intron of the X-chromosomal allele of the Xmrk proto-oncogene, and a second, more corrupted copy is present only 56 nt downstream of the polyadenylation signal of the Xmrk oncogene. Jule-related elements were detected by Southern blot hybridization with less than 10 copies per haploid genome in numerous other poeciliids, as well as in more divergent fishes, including the medakafish Oryzias latipes and the tilapia Oreochromis niloticus. Database searches also identified Jule-related sequences in the zebrafish Danio rerio and in both genome project pufferfishes, Fugu rubripes and Tetraodon nigroviridis. Phylogenetic analysis revealed that Jule is the first member of the Mag family of Ty3/Gypsy retrotransposons described to date in vertebrates. This family includes the silkworm Mag and sea urchin SURL retrotransposons, as well as sequences from the nematode Caenorhabditis elegans. Additional related elements were identified in the genomes of the malaria mosquito Anopheles gambiae and the nematode Ascaris lumbricoides. Phylogeny of Mag-related elements suggested that the Mag family of retrotransposons is polyphyletic and is constituted of several ancient lineages that diverged before their host genomes more than 600 MYA. PMID

  2. Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons

    PubMed Central

    Albert, Patrice S.; Koo, Dal-Hoe; Shi, Jinghua; Gao, Zhi; Han, Fangpu; Lee, Hyeran; Xu, Ronghui; Allison, Jamie; Birchler, James A.; Jiang, Jiming; Dawe, R. Kelly; Presting, Gernot G.

    2009-01-01

    We describe a comprehensive and general approach for mapping centromeres and present a detailed characterization of two maize centromeres. Centromeres are difficult to map and analyze because they consist primarily of repetitive DNA sequences, which in maize are the tandem satellite repeat CentC and interspersed centromeric retrotransposons of maize (CRM). Centromeres are defined epigenetically by the centromeric histone H3 variant, CENH3. Using novel markers derived from centromere repeats, we have mapped all ten centromeres onto the physical and genetic maps of maize. We were able to completely traverse centromeres 2 and 5, confirm physical maps by fluorescence in situ hybridization (FISH), and delineate their functional regions by chromatin immunoprecipitation (ChIP) with anti-CENH3 antibody followed by pyrosequencing. These two centromeres differ substantially in size, apparent CENH3 density, and arrangement of centromeric repeats; and they are larger than the rice centromeres characterized to date. Furthermore, centromere 5 consists of two distinct CENH3 domains that are separated by several megabases. Succession of centromere repeat classes is evidenced by the fact that elements belonging to the recently active recombinant subgroups of CRM1 colonize the present day centromeres, while elements of the ancestral subgroups are also found in the flanking regions. Using abundant CRM and non-CRM retrotransposons that inserted in and near these two centromeres to create a historical record of centromere location, we show that maize centromeres are fluid genomic regions whose borders are heavily influenced by the interplay of retrotransposons and epigenetic marks. Furthermore, we propose that CRMs may be involved in removal of centromeric DNA (specifically CentC), invasion of centromeres by non-CRM retrotransposons, and local repositioning of the CENH3. PMID:19956743

  3. A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes

    PubMed Central

    Iwasaki, Yukimoto; Kitano, Hidemi; Itoh, Jun-Ichi; Maekawa, Masahiko; Murata, Kazumasa; Yatou, Osamu; Nagato, Yasuo; Hirochika, Hirohiko

    2006-01-01

    In order to facilitate the functional analysis of rice genes, we produced about 50,000 insertion lines with the endogenous retrotransposon Tos17. Phenotypes of these lines in the M2 generation were observed in the field and characterized based on 53 phenotype descriptors. Nearly half of the lines showed more than one mutant phenotype. The most frequently observed phenotype was low fertility, followed by dwarfism. Phenotype data with photographs of each line are stored in the Tos17 mutant panel web-based database with a dataset of sequences flanking Tos17 insertion points in the rice genome (http://tos.nias.affrc.go.jp/). This combination of phenotypic and flanking sequence data will stimulate the functional analysis of rice genes. PMID:17180734

  4. Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease

    PubMed Central

    Govindaraju, Aruna; Cortez, Jeremy D.; Reveal, Brad; Christensen, Shawn M.

    2016-01-01

    Non-LTR retrotransposons are an important class of mobile elements that insert into host DNA by target-primed reverse transcription (TPRT). Non-LTR retrotransposons must bind to their mRNA, recognize and cleave their target DNA, and perform TPRT at the site of DNA cleavage. As DNA binding and cleavage are such central parts of the integration reaction, a better understanding of the endonuclease encoded by non-LTR retrotransposons is needed. This paper explores the R2 endonuclease domain from Bombyx mori using in vitro studies and in silico modeling. Mutations in conserved sequences located across the putative PD-(D/E)XK endonuclease domain reduced DNA cleavage, DNA binding and TPRT. A mutation at the beginning of the first α-helix of the modeled endonuclease obliterated DNA cleavage and greatly reduced DNA binding. It also reduced TPRT when tested on pre-cleaved DNA substrates. The catalytic K was located to a non-canonical position within the second α-helix. A mutation located after the fourth β-strand reduced DNA binding and cleavage. The motifs that showed impaired activity form an extensive basic region. The R2 biochemical and structural data are compared and contrasted with that of two other well characterized PD-(D/E)XK endonucleases, restriction endonucleases and archaeal Holliday junction resolvases. PMID:26961309

  5. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.

    PubMed

    Kojima, Kenji K; Jurka, Jerzy

    2015-01-01

    Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes. PMID:26556480

  6. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia

    PubMed Central

    Kojima, Kenji K.

    2015-01-01

    Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an “archaeal” RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes. PMID:26556480

  7. The genomic organization of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms.

    PubMed

    Kubis, S E; Heslop-Harrison, J S; Desel, C; Schmidt, T

    1998-04-01

    We have isolated and characterized conserved regions of the reverse transcriptase gene from non-LTR retrotransposons, also called long interspersed nuclear elements (LINEs), from Beta vulgaris, B. lomatogona and B. nana. The novel elements show strong homology to other non-LTR retrotransposons from plants, man and animals. LINEs are present in all species of the genus Beta tested, but there was variation in copy number. Analysis by Southern hybridization and fluorescent in situ hybridization revealed the clustered organization of these retroelements in beet species. PCR amplification using degenerate primers to conserved motifs of the predicted LINE protein sequence enabled the cloning of LINEs from both Monocotyledonae (Allium cepa, Oryza sativa and Secale cereale) and Dicotyledonae (Nicotiana tabacum and Antirrhinum majus) indicating that LINEs are a universal feature of plant genomes. A dendrogram of fifteen new and six previously isolated sequences showed the high level of sequence divergence while revealing families characteristic of some genera. The genomic organization of non-LTR retrotransposons was examined more detailed in A. majus and O. sativa. PMID:9520275

  8. Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing

    PubMed Central

    Monden, Yuki; Hara, Takuya; Okada, Yoshihiro; Jahana, Osamu; Kobayashi, Akira; Tabuchi, Hiroaki; Onaga, Shoko; Tahara, Makoto

    2015-01-01

    Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90). Although sweetpotato is one of the world’s most important crops, genetic analysis of the species has been hindered by its genetic complexity combined with the lack of a whole genome sequence. In the present study, we constructed a genetic linkage map based on retrotransposon insertion polymorphisms using a mapping population derived from a cross between ‘Purple Sweet Lord’ (PSL) and ‘90IDN-47’ cultivars. High-throughput sequencing and subsequent data analyses identified many Rtsp-1 retrotransposon insertion sites, and their allele dosages (simplex, duplex, triplex, or double-simplex) were determined based on segregation ratios in the mapping population. Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively. Interestingly, most of these insertions (~90%) were present in a simplex manner, indicating their utility for linkage map construction in polyploid species. Additionally, our approach led to savings of time and labor for genotyping. Although the number of markers herein was insufficient for map-based cloning, our trial analysis exhibited the utility of retrotransposon-based markers for linkage map construction in sweetpotato. PMID:26069444

  9. The Wukong Terminal-Repeat Retrotransposon in Miniature (TRIM) Elements in Diverse Maize Germplasm

    PubMed Central

    Liu, Zhen; Li, Xinxin; Wang, Tingzhang; Messing, Joachim; Xu, Jian-Hong

    2015-01-01

    TRIMs (terminal-repeat retrotransposons in miniature), which are characterized by their small size, have been discovered in all investigated vascular plants and even in animals. Here, we identified a highly conservative TRIM family referred to as Wukong elements in the maize genome. The Wukong family shows a distinct pattern of tandem arrangement in the maize genome suggesting a high rate of unequal crossing over. Estimation of insertion times implies a burst of retrotransposition activity of the Wukong family after the allotetraploidization of maize. Using next-generation sequencing data, we detected 87 new Wukong insertions in parents of the maize NAM population relative to the B73 reference genome and found abundant insertion polymorphism of Wukong elements in 75 re-sequenced maize lines, including teosinte, landraces, and improved lines. These results suggest that Wukong elements possessed a persistent retrotransposition activity throughout maize evolution. Moreover, the phylogenetic relationships among 76 maize inbreds and their relatives based on insertion polymorphisms of Wukong elements should provide us with reliable molecular markers for biodiversity and genetics studies. PMID:26019188

  10. Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation

    PubMed Central

    Senerchia, Natacha; Felber, François; Parisod, Christian

    2015-01-01

    Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation. PMID:25716787

  11. Transposition of the retrotransposon MAGGY in heterologous species of filamentous fungi.

    PubMed Central

    Nakayashiki, H; Kiyotomi, K; Tosa, Y; Mayama, S

    1999-01-01

    MAGGY is a gypsy-like LTR retrotransposon isolated from the blast fungus Pyricularia grisea (teleomorph, Magnaporthe grisea). We examined transposition of MAGGY in three P. grisea isolates (wheat, finger millet, and crabgrass pathogen), which did not originally possess a MAGGY element, and in two heterologous species of filamentous fungi, Colletotrichum lagenarium and P. zingiberi. Genomic Southern analysis of MAGGY transformants suggested that transposition of MAGGY occurred in all filamentous fungi tested. In contrast, no transposition was observed in any transformants with a modified MAGGY containing a 513-bp deletion in the reverse transcriptase domain. When a MAGGY derivative carrying an artificial intron was introduced into the wheat isolate of P. grisea and C. lagenarium, loss of the intron was observed. These results showed that MAGGY can undergo autonomous RNA-mediated transposition in heterologous filamentous fungi. The frequency of transposition differed among fungal species. MAGGY transposed actively in the wheat isolate of P. grisea and P. zingiberi, but transposition in C. lagenarium appeared to be rare. This is the first report that demonstrates active transposition of a fungal transposable element in heterologous hosts. Possible usage of MAGGY as a genetic tagging tool in filamentous fungi is discussed. PMID:10511549

  12. Coordination of transposon expression with DNA replication in the targeting of telomeric retrotransposons in Drosophila

    PubMed Central

    Zhang, Liang; Beaucher, Michelle; Cheng, Yan; Rong, Yikang S

    2014-01-01

    In Drosophila, a group of retrotransposons is mobilized exclusively to telomeres in a sequence-independent manner. How they target chromosome ends is not understood. Here, we focused on the telomeric element HeT-A and characterized the cell cycle expression and cytological distribution of its protein and RNA products. We determined the timing of telomere replication by creating a single lacO-marked telomere and provide evidence suggesting that transposon expression and recruitment to telomeres is linked to telomere replication. The HeT-A-encoded ORF1p protein is expressed predominantly in S phase, particularly in early S phase. Orf1p binds HeT-A transcripts and forms spherical structures at telomeres undergoing DNA replication. HeT-A sphere formation requires Verrocchio, a putative homolog of the conserved Stn1 telomeric protein. Our results suggest that coupling of telomere elongation and telomere replication is a universal feature, and raise the possibility that transposon recruitment to Drosophila telomeres is mechanistically related to telomerase recruitment in other organisms. Our study also supports a co-adaptive relationship between the Drosophila host and HeT-A mobile elements. PMID:24733842

  13. Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat.

    PubMed

    Kraitshtein, Zina; Yaakov, Beery; Khasdan, Vadim; Kashkush, Khalil

    2010-11-01

    Allopolyploidy, or the combination of two or more distinct genomes in one nucleus, is usually accompanied by radical genomic changes involving transposable elements (TEs). The dynamics of TEs after an allopolyploidization event are poorly understood. In this study, we analyzed the methylation state and genetic rearrangements of a high copied, newly amplified terminal-repeat retrotransposon in miniature (TRIM) family in wheat termed Veju. We found that Veju insertion sites underwent massive methylation changes in the first four generations of a newly formed wheat allohexaploid. Hypomethylation or hypermethylation occurred in ∼43% of the tested insertion sites; while hypomethylation was significantly predominant in the first three generations of the newly formed allohexaploid, hypermethylation became predominant in the subsequent generation. In addition, we determined that the methylation state of Veju long terminal repeats (LTRs) might be correlated with the deletion and/or insertion of the TE. While most of the methylation changes and deletions of Veju occurred in the first generation of the newly formed allohexaploid, most Veju insertions were seen in the second generation. Finally, using quantitative PCR, we quantitatively assessed the genome composition of Veju in the newly formed allohexaploid and found that up to 50% of Veju LTRs were deleted in the first generation. Retrotransposition bursts in subsequent generations, however, led to increases in Veju elements. In light of these findings, the underlying mechanisms of TRIM rearrangements are discussed. PMID:20823338

  14. Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats.

    PubMed

    Senerchia, Natacha; Felber, François; North, Béatrice; Sarr, Anouk; Guadagnuolo, Roberto; Parisod, Christian

    2016-06-01

    The maintenance of species integrity despite pervasive hybridization is ruled by the interplay between reproductive barriers. Endogenous postzygotic isolation will shape the patterns of introgression in hybrid zones, leading to variable outcomes depending on the genetic mechanism involved. Here, we analysed experimental and natural hybrid populations of Aegilops geniculata and Aegilops triuncialis to examine the genetics of species boundaries in the face of gene flow. Because long-terminal repeat retrotransposons (LTR-RTs) showing differential evolutionary trajectories are probably to affect hybrid dysgenesis and reproductive isolation between these wild wheat species, we addressed the impact of LTR-RTs in shaping introgression between them. Experimental settings involving artificial sympatry and enforced crossings quantified strong, but incomplete reproductive isolation, and highlighted asymmetrical endogenous postzygotic isolation between the two species. Natural hybrid zones located in the northern Golan Heights were analysed using plastid DNA, amplified fragment length polymorphisms (AFLP) marking random sequences, and sequence-specific amplified polymorphisms (SSAP) tracking insertions from six LTR-RT families. This analysis demonstrated asymmetrical introgression and genome reorganization. In comparison with random sequences and quiescent LTR-RTs, those LTR-RTs predicted to be activated following conflicting interactions in hybrids revealed differential introgression across the hybrid zones. As also reported for synthetic F1 hybrids, such LTR-RTs were specifically reorganized in the genomes of viable hybrids, confirming that conflicts between selfish LTR-RTs may represent key incompatibilities shaping species boundaries and fostering long-term species integrity in the face of gene flow. PMID:26678573

  15. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci

    PubMed Central

    Philippe, Claude; Vargas-Landin, Dulce B; Doucet, Aurélien J; van Essen, Dominic; Vera-Otarola, Jorge; Kuciak, Monika; Corbin, Antoine; Nigumann, Pilvi; Cristofari, Gaël

    2016-01-01

    LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants. DOI: http://dx.doi.org/10.7554/eLife.13926.001 PMID:27016617

  16. Serial number tagging reveals a prominent sequence preference of retrotransposon integration.

    PubMed

    Chatterjee, Atreyi Ghatak; Esnault, Caroline; Guo, Yabin; Hung, Stevephen; McQueen, Philip G; Levin, Henry L

    2014-07-01

    Transposable elements (TE) have both negative and positive impact on the biology of their host. As a result, a balance is struck between the host and the TE that relies on directing integration to specific genome territories. The extraordinary capacity of DNA sequencing can create ultra dense maps of integration that are being used to study the mechanisms that position integration. Unfortunately, the great increase in the numbers of insertion sites detected comes with the cost of not knowing which positions are rare targets and which sustain high numbers of insertions. To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions. We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position. Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration. The serial number system is a general method that can be applied to determine precise integration maps for retroviruses and gene therapy vectors. PMID:24948612

  17. Spontaneous retrotransposon insertion into TNF 3'UTR causes heart valve disease and chronic polyarthritis.

    PubMed

    Lacey, Derek; Hickey, Peter; Arhatari, Benedicta D; O'Reilly, Lorraine A; Rohrbeck, Leona; Kiriazis, Helen; Du, Xiao-Jun; Bouillet, Philippe

    2015-08-01

    Rheumatoid arthritis (RA) and ankylosing spondylitis (AS) are chronic inflammatory diseases that together affect 2-3% of the population. RA and AS predominantly involve joints, but heart disease is also a common feature in RA and AS patients. Here we have studied a new spontaneous mutation that causes severe polyarthritis in bone phenotype spontaneous mutation 1 (BPSM1) mice. In addition to joint destruction, mutant mice also develop aortic root aneurism and aorto-mitral valve disease that can be fatal depending on the genetic background. The cause of the disease is the spontaneous insertion of a retrotransposon into the 3' untranslated region (3'UTR) of the tumor necrosis factor (TNF), which triggers its strong overexpression in myeloid cells. We found that several members of a family of RNA-binding, CCCH-containing zinc-finger proteins control TNF expression through its 3'UTR, and we identified a previously unidentified regulatory element in the UTR. The disease in BPSM1 mice is independent of the adaptive immune system and does not appear to involve inflammatory cytokines other than TNF. To our knowledge, this is the first animal model showing both polyarthritis and heart disease as a direct result of TNF deregulation. These results emphasize the therapeutic potential of anti-TNF drugs for the treatment of heart valve disease and identify potential therapeutic targets to control TNF expression and inflammation. PMID:26195802

  18. Possible regulatory function of the Saccharomyces cerevisiae Ty1 retrotransposon core protein.

    PubMed

    Roth, J F; Kingsman, S M; Kingsman, A J; Martin-Rendon, E

    2000-07-01

    The yeast Ty1 retrotransposon encodes proteins and RNA that assemble into virus-like particles (VLPs) as part of the life cycle of the retro-element. The Tya protein, which is equivalent to the retroviral Gag, is the major structural component of these particles. In this work, we demonstrate that Tya proteins fulfil other functions apart from their structural role. We show that Tya interacts in vitro with the Ty1 RNA domain required for RNA packaging, suggesting that this RNA-protein interaction may direct the packaging process. Furthermore, the overexpression of both Tya proteins, i.e. p1, the primary translation product, and p2, the mature form, increases endogenous Ty1 RNA levels in trans without increasing translation significantly. These observations suggest that Tya may exert a regulatory function during transposition. Interestingly, however, only p2, the mature form of Tya, trans-activates transposition of a marked genomic Ty element. This confirms that processing is required for transposition. PMID:10870103

  19. The Drosophila micropia retrotransposon encodes a testis-specific antisense RNA complementary to reverse transcriptase.

    PubMed Central

    Lankenau, S; Corces, V G; Lankenau, D H

    1994-01-01

    The micropia transposable element of Drosophila hydei is a long terminal repeat-containing retrotransposon present in both the autosomes and the Y chromosome. micropia expression gives rise to a complex set of sense and antisense RNAs transcribed primarily during spermatogenesis. The most abundant sense RNAs constitute an assortment of heterogeneous high-molecular-weight transcripts expressed as constituents of the Y-chromosomal lampbrush loops of primary spermatocytes. In addition, micropia encodes a full-length RNA that extends between the two long terminal repeats of the element. The major 1.0-kb antisense RNA characterized is complementary to the reverse transcriptase and RNase H coding regions of micropia. It is expressed from a testis-specific promoter during the primary spermatocyte stages and is detectable until spermatid elongation stages. Sequence comparison of this promoter with the 5' region of other testis-specific genes allows the conception of a conserved sequence that is responsible for this pattern of expression. A 284-bp fragment containing this sequence is able to drive testis-specific expression of the Escherichia coli lacZ gene in Drosophila melanogaster. This sequence is conserved in the micropia elements present in other Drosophila species that also encode an antisense RNA. The evolutionary conservation of micropia antisense RNA expression and the sequences responsible for its testis-specific transcription suggests a role for this antisense RNA in the control of germ line expression of the full-length transcript or transposon-encoded proteins. Images PMID:7509447

  20. Spontaneous retrotransposon insertion into TNF 3′UTR causes heart valve disease and chronic polyarthritis

    PubMed Central

    Lacey, Derek; Hickey, Peter; Arhatari, Benedicta D.; O’Reilly, Lorraine A.; Rohrbeck, Leona; Kiriazis, Helen; Du, Xiao-Jun; Bouillet, Philippe

    2015-01-01

    Rheumatoid arthritis (RA) and ankylosing spondylitis (AS) are chronic inflammatory diseases that together affect 2–3% of the population. RA and AS predominantly involve joints, but heart disease is also a common feature in RA and AS patients. Here we have studied a new spontaneous mutation that causes severe polyarthritis in bone phenotype spontaneous mutation 1 (BPSM1) mice. In addition to joint destruction, mutant mice also develop aortic root aneurism and aorto-mitral valve disease that can be fatal depending on the genetic background. The cause of the disease is the spontaneous insertion of a retrotransposon into the 3′ untranslated region (3′UTR) of the tumor necrosis factor (TNF), which triggers its strong overexpression in myeloid cells. We found that several members of a family of RNA-binding, CCCH-containing zinc-finger proteins control TNF expression through its 3′UTR, and we identified a previously unidentified regulatory element in the UTR. The disease in BPSM1 mice is independent of the adaptive immune system and does not appear to involve inflammatory cytokines other than TNF. To our knowledge, this is the first animal model showing both polyarthritis and heart disease as a direct result of TNF deregulation. These results emphasize the therapeutic potential of anti-TNF drugs for the treatment of heart valve disease and identify potential therapeutic targets to control TNF expression and inflammation. PMID:26195802

  1. An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris.

    PubMed

    Wenke, Torsten; Holtgräwe, Daniela; Horn, Axel V; Weisshaar, Bernd; Schmidt, Thomas

    2009-12-01

    We describe a non-LTR retrotransposon family,BvL, of the long interspersed nuclear elements L1 clade isolated from sugar beet (Beta vulgaris). Characteristic molecular domains of three full-length BvL elements were determined in detail, showing that coding sequences are interrupted and most likely non-functionally. In addition,eight highly conserved endonuclease regions were defined by comparison with other plant LINEs. The abundant BvL family is widespread within the genus Beta, however, the vast majority of BvL copies are extremely 50 truncated indicating an error-prone reverse transcriptase activity. The dispersed distribution of BvL copies on all sugar beet chromosomes with exclusion of most heterochromatic regions was shown by fluorescent in situ hybridization. The analysis of BvL 30 end sequences and corresponding flanking regions, respectively, revealed the preferred integration of BvL into A/T-rich regions of the sugar beet genome, but no specific target sequences. PMID:19697140

  2. Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation.

    PubMed

    Senerchia, Natacha; Felber, François; Parisod, Christian

    2015-04-01

    Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation. PMID:25716787

  3. Structure Prediction and Analysis of DNA Transposon and LINE Retrotransposon Proteins*

    PubMed Central

    Abrusán, György; Zhang, Yang; Szilágyi, András

    2013-01-01

    Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology. PMID:23530042

  4. Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing

    PubMed Central

    Bakshi, Arundhati; Ekram, Muhammad B.; Kim, Joomyeong

    2014-01-01

    DNA methylation is a major epigenetic mark associated with multiple aspects of retrotransposons within the mammalian genome. In order to study DNA methylation of a large number of retrotransposons on an individual-locus basis, we have developed a new protocol termed High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS) (Ekram and Kim, 2014 [1]). We have used this technique to characterize the locus-specific patterns of DNA methylation of 4799 members of the mouse IAP LTR (Intracisternal A Particle Long Terminal Repeat) retrotransposon family in embryonic stem, somatic and Neuro2A cells (Bakshi and Kim, 2014 [2]). Here we describe in detail the sample preparation and bioinformatics analyses used for these studies. The somatic cell data may be accessed under GEO accession number GSE49222. The ES and Neuro2A data are deposited under GEO accession number GSE60007. PMID:25554740

  5. Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

    PubMed Central

    Tollis, Marc; Boissinot, Stéphane

    2013-01-01

    Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, originally proposed in Drosophila, applies to nonmammalian vertebrates. Here, we studied the population dynamics of L1 in the green anole lizard (Anolis carolinensis). We found that although most L1 elements are recent in this genome, truncated insertions accumulate readily, and many are fixed at both the population and species level. In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis. We also found that full-length L1 inserts are more likely to be fixed in populations of small effective size, suggesting that the strength of purifying selection against deleterious alleles is highly dependent on host demographic history. Similar mechanisms seem to be controlling the fate of non-LTR retrotransposons in both Anolis and teleostean fish, which suggests that mammals have considerably diverged from the ancestral vertebrate in terms of how they interact with their intragenomic parasites. PMID:24013105

  6. Curiously composite structures of a retrotransposon and a complex repeat associated with chromosome ends of Rhynchosciara americana (Diptera: Sciaridae).

    PubMed

    Madalena, Christiane Rodriguez Gutierrez; Fernandes, Thiago; Villasante, Alfredo; Gorab, Eduardo

    2010-07-01

    In Drosophila, telomere retrotransposons counterbalance the loss of telomeric DNA. The exceptional mechanism of telomere recovery characterized in Drosophila has not been found in lower dipterans (Nematocera). However, a retroelement resembling a telomere transposon and termed "RaTART" has been described in the nematoceran Rhynchosciara americana. In this work, DNA and protein sequence analyses, DNA cloning, and chromosomal localization of probes obtained either by PCR or by screening a genomic library were carried out in order to examine additional features of this retroelement. The analyses performed raise the possibility that RaTART represents a genomic clone composed of distinct repetitive elements, one of which is likely to be responsible for its apparent enrichment at chromosome ends. RaTART sequence in addition allowed to assess a novel subtelomeric region of R. americana chromosomes that was analyzed in this work after subcloning a DNA fragment from a phage insert. It contains a complex repeat that is located in the vicinity of simple and complex tandem repeats characterized previously. Quantification data suggest that the copy number of the repeat is significantly lower than that observed for the ribosomal DNA in the salivary gland of R. americana. A short insertion of the RaTART was identified in the cloned segment, which hybridized preferentially to subtelomeres. Like RaTART, it displays truncated sequences related to distinct retrotransposons, one of which has a conceptual translation product with significant identity with an endonuclease from a lepidopteran retrotransposon. The composite structure of this DNA stretch probably reflects mobile element activity in the subtelomeric region analyzed in this work. PMID:20607598

  7. Mapping of retrotransposon sequences in the unstable region surrounding the spinal muscular atrophy locus in 5q13

    SciTech Connect

    Francis, M.J.; Nesbit, M.A.; Theodosiou, A.M.

    1995-05-20

    The mutation that underlies the autosomal recessive disorder spinal muscular atrophy (SMA) is located on chromosome 5q13. Recent studies show that SMA patients frequently have deletions and rearrangements in this region compared to normal controls. During the isolation of candidate cDNAs for the disease, the authors identified a sequence that shows high homology to the THE-1 retrotransposon gene family. Using YAC fragmentation techniques, they have refined the localization of this sequence to the domain known to show instability in SMA patients. The implication of these results for the mechanism of the mutation in SMA is discussed. 20 refs., 1 fig.

  8. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration

    PubMed Central

    Zhu, Wei; Kuo, Dwight; Nathanson, Jason; Satoh, Akira; Pao, Gerald M.; Yeo, Gene W.; Bryant, Susan V.; Voss, S. Randal; Gardiner, David M.; Hunter, Tony

    2012-01-01

    Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes within the Mexican axolotl (Ambystoma mexicanum) that is indicative of cellular reprogramming of differentiated cells into a germline-like state. In this work, we focus on one of these genes, the long interspersed nucleotide element-1 (LINE-1) retrotransposon, which is usually active in germ cells and silent in most of the somatic tissues in other organisms. LINE-1 was found to be dramatically upregulated during regeneration. In addition, higher genomic LINE-1 content was also detected in the limb regenerate when compared to that before amputation indicating that LINE-1 retrotransposition is indeed active during regeneration. Active LINE-1 retrotransposition has been suggested to have a potentially deleterious impact on genomic integrity. Silencing of activated LINE-1 by small RNAs has been reported to be part of the machinery aiming to maintain genomic integrity. Indeed, we were able to identify putative LINE-1-related piRNAs in the limb blastema. Transposable element-related piRNAs have been identified frequently in the germline in other organisms. Thus, we present here a scenario in which a unique germline-like state is established during axolotl limb regeneration, and the re-activation of LINE-1 may serve as a marker for cellular dedifferentiation in the early-stage of limb regeneration. PMID:22913491

  9. Evolutionary Dynamics of the Ty3/Gypsy LTR Retrotransposons in the Genome of Anopheles gambiae

    PubMed Central

    Tubio, Jose Manuel C.; Tojo, Marta; Bassaganyas, Laia; Escaramis, Georgia; Sharakhov, Igor V.; Sharakhova, Maria V.; Tornador, Cristian; Unger, Maria F.; Naveira, Horacio; Costas, Javier; Besansky, Nora J.

    2011-01-01

    Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr) groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis. PMID:21283637

  10. Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning

    PubMed Central

    2011-01-01

    Background Unique structural characteristics of centromere chromatin enable it to support assembly of the kinetochore and its associated tensions. The histone H3 variant CENH3 (centromeric histone H3) is viewed as the key element of centromere chromatin and its interaction with centromere DNA is epigenetic in that its localization to centromeres is not sequence-dependent. Results In order to investigate what influence the DNA sequence exerts on CENH3 chromatin structure, we examined CENH3 nucleosome footprints on maize centromere DNA. We found a predominant average nucleosome spacing pattern of roughly 190-bp intervals, which was also the dominant arrangement for nucleosomes genome-wide. For CENH3-containing nucleosomes, distinct modes of nucleosome positioning were evident within that general spacing constraint. Over arrays of the major ~156-bp centromeric satellite sequence (tandem repeat) CentC, nucleosomes were not positioned in register with CentC monomers but in conformity with a striking ~10-bp periodicity of AA/TT dimers within the sequence. In contrast, nucleosomes on a class of centromeric retrotransposon (CRM2) lacked a detectable AA/TT periodicity but exhibited tightly phased positioning. Conclusions These data support a model in which general chromatin factors independent of both DNA sequence and CENH3 enforce roughly uniform centromeric nucleosome spacing while allowing flexibility in the mode in which nucleosomes are positioned. In the case of tandem repeat DNA, the natural bending effects related to AA/TT periodicity produce an energetically-favourable arrangement consistent with conformationally rigid nucleosomes and stable chromatin at centromeres. PMID:21352520

  11. Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids.

    PubMed

    Romero-Soriano, Valèria; Garcia Guerreiro, Maria Pilar

    2016-01-01

    Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii-D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny. PMID:26812285

  12. Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

    PubMed Central

    Romero-Soriano, Valèria; Garcia Guerreiro, Maria Pilar

    2016-01-01

    Transposable elements (TEs), repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA) pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii—D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny. PMID:26812285

  13. Control of gag-pol gene expression in the Candida albicans retrotransposon Tca2

    PubMed Central

    Forbes, Elaine M; Nieduszynska, Siân R; Brunton, Fiona K; Gibson, Joanne; Glover, L Anne; Stansfield, Ian

    2007-01-01

    Background In the C. albicans retrotransposon Tca2, the gag and pol ORFs are separated by a UGA stop codon, 3' of which is a potential RNA pseudoknot. It is unclear how the Tca2 gag UGA codon is bypassed to allow pol expression. However, in other retroelements, translational readthrough of the gag stop codon can be directed by its flanking sequence, including a 3' pseudoknot. Results The hypothesis was tested that in Tca2, gag stop codon flanking sequences direct translational readthrough and synthesis of a gag-pol fusion protein. Sequence from the Tca2 gag-UGA-pol junction (300 nt) was inserted between fused lacZ and luciferase (luc) genes in a Saccharomyces cerevisiae dual reporter construct. Although downstream of UGA, luc was expressed, but its expression was unaffected by inserting additional stop codons at the 3' end of lacZ. Luc expression was instead being driven by a previously unknown minor promoter activity within the gag-pol junction region. Evidence together indicated that junction sequence alone cannot direct UGA readthrough. Using reporter genes in C. albicans, the activities of this gag-pol junction promoter and the Tca2 long terminal repeat (LTR) promoter were compared. Of the two promoters, only the LTR promoter was induced by heat-shock, which also triggers retrotransposition. Tca2 pol protein, epitope-tagged in C. albicans to allow detection, was also heat-shock induced, indicating that pol proteins were expressed from a gag-UGA-pol RNA. Conclusion This is the first demonstration that the LTR promoter directs Tca2 pol protein expression, and that pol proteins are translated from a gag-pol RNA, which thus requires a mechanism for stop codon bypass. However, in contrast to most other retroelement and viral readthrough signals, immediate gag UGA-flanking sequences were insufficient to direct stop readthrough in S. cerevisiae, indicating non-canonical mechanisms direct gag UGA bypass in Tca2. PMID:17961216

  14. Evolution of the R2 Retrotransposon Ribozyme and Its Self-Cleavage Site

    PubMed Central

    Eickbush, Danna G.; Burke, William D.; Eickbush, Thomas H.

    2013-01-01

    R2 is a non-long terminal repeat retrotransposon that inserts site-specifically in the tandem 28S rRNA genes of many animals. Previously, R2 RNA from various species of Drosophila was shown to self-cleave from the 28S rRNA/R2 co-transcript by a hepatitis D virus (HDV)-like ribozyme encoded at its 5' end. RNA cleavage was at the precise 5' junction of the element with the 28S gene. Here we report that RNAs encompassing the 5' ends of R2 elements from throughout its species range fold into HDV-like ribozymes. In vitro assays of RNA self-cleavage conducted in many R2 lineages confirmed activity. For many R2s, RNA self-cleavage was not at the 5' end of the element but at 28S rRNA sequences up to 36 nucleotides upstream of the junction. The location of cleavage correlated well with the types of endogenous R2 5' junctions from different species. R2 5' junctions were uniform for most R2s in which RNA cleavage was upstream in the rRNA sequences. The 28S sequences remaining on the first DNA strand synthesized during retrotransposition are postulated to anneal to the target site and uniformly prime second strand DNA synthesis. In species where RNA cleavage occurred at the R2 5' end, the 5' junctions were variable. This junction variation is postulated to result from the priming of second strand DNA synthesis by chance microhomologies between the target site and the first DNA strand. Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed. PMID:24066021

  15. The Reverse Transcriptase Encoded by LINE-1 Retrotransposons in the Genesis, Progression, and Therapy of Cancer

    PubMed Central

    Sciamanna, Ilaria; De Luca, Chiara; Spadafora, Corrado

    2016-01-01

    In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons represent a large family of repeated genomic elements. They transpose using a reverse transcriptase (RT), which they encode as part of the ORF2p product. RT inhibition in cancer cells, either via RNA interference-dependent silencing of active LINE-1 elements, or using RT inhibitory drugs, reduces cancer cell proliferation, promotes their differentiation and antagonizes tumor progression in animal models. Indeed, the non-nucleoside RT inhibitor efavirenz has recently been tested in a phase II clinical trial with metastatic prostate cancer patients. An in-depth analysis of ORF2p in a mouse model of breast cancer showed ORF2p to be precociously expressed in precancerous lesions and highly abundant in advanced cancer stages, while being barely detectable in normal breast tissue, providing a rationale for the finding that RT-expressing tumors are therapeutically sensitive to RT inhibitors. We summarize mechanistic and gene profiling studies indicating that abundant LINE-1-derived RT can “sequester” RNA substrates for reverse transcription in tumor cells, entailing the formation of RNA:DNA hybrid molecules and impairing the overall production of regulatory miRNAs, with a global impact on the cell transcriptome. Based on these data, LINE-1-ORF2 encoded RT has a tumor-promoting potential that is exerted at an epigenetic level. We propose a model whereby LINE1-RT drives a previously unrecognized global regulatory process, the deregulation of which drives cell transformation and tumorigenesis with possible implications for cancer cell heterogeneity. PMID:26904537

  16. Evolution of diverse mechanisms for protecting chromosome ends by Drosophila TART telomere retrotransposons

    PubMed Central

    George, Janet A.; Traverse, Karen L.; DeBaryshe, P. G.; Kelley, Kerry J.; Pardue, Mary-Lou

    2010-01-01

    The retrotransposons HeT-A, TART, and TAHRE, which maintain Drosophila telomeres, transpose specifically onto chromosome ends to form long arrays that extend the chromosome and compensate for terminal loss. Because they transpose by target-primed reverse transcription, each element is oriented so that its 5′ end serves as the extreme end of the chromosome until another element transposes to occupy the terminal position. Thus 5′ sequences are at risk for terminal erosion while the element is at the chromosome end. Here we report that TART elements in Drosophila melanogaster and Drosophila virilis show species-specific innovations in promoter architecture that buffer loss of sequence exposed at chromosome ends. The two elements have evolved different ways to effect this protection. The D. virilis TART (TARTvir) promoter is found in the 3′ UTR of the element directly upstream of the element transcribed. Transcription starts within the upstream element so that a “Tag” of extra sequence is added to the 5′ end of the newly transcribed RNA. This Tag provides expendable sequence to buffer end erosion of essential 5′ sequence after the RNA is reverse transcribed onto the chromosome. In contrast, the D. melanogaster TART (TARTmel) promoter initiates transcription deep within the 5′ UTR, but the element is able to replace and extend the 5′ UTR sequence by copying sequence from its 3′ UTR, we believe while being reverse transcribed onto the chromosome end. Astonishingly, end-protection in TARTvir and HeT-Amel are essentially identical (using Tags), whereas HeT-Avir is clearly protected from end erosion by an as-yet-unspecified program. PMID:21088221

  17. The reverse transcriptase encoded by LINE-1 retrotransposons in the genesis, progression and therapy of cancer

    NASA Astrophysics Data System (ADS)

    Sciamanna, Ilaria; De Luca, Chiara; Spadafora, Corrado

    2016-02-01

    In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons represent a large family of repeated genomic elements. They transpose using a reverse transcriptase (RT), which they encode as part of the ORF2p product. RT inhibition in cancer cells, either via RNA interference-dependent silencing of active LINE-1 elements, or using RT inhibitory drugs, reduces cancer cell proliferation, promotes their differentiation and antagonizes tumor progression in animal models. Indeed, the nonnucleoside RT inhibitor efavirenz has recently been tested in a phase II clinical trial with metastatic prostate cancer patients. An in-depth analysis of ORF2p in a mouse model of breast cancer showed ORF2p to be precociously expressed in precancerous lesions and highly abundant in advanced cancer stages, while being barely detectable in normal breast tissue, providing a rationale for the finding that RT-expressing tumours are therapeutically sensitive to RT inhibitors. We summarise mechanistic and gene profiling studies indicating that highly abundant LINE-1-derived RT can “sequester” RNA substrates for reverse transcription in tumor cells, entailing the formation of RNA:DNA hybrid molecules and impairing the overall production of regulatory miRNAs, with a global impact on the cell transcriptome. Based on these data, LINE-1-ORF2 encoded RT has a tumor-promoting potential that is exerted at an epigenetic level. We propose a model whereby LINE1-RT drives a previously unrecognized global regulatory process, the deregulation of which drives cell transformation and tumorigenesis and possibly implicated in cancer cell heterogeneity.

  18. Mammalian-specific genomic functions: Newly acquired traits generated by genomic imprinting and LTR retrotransposon-derived genes in mammals

    PubMed Central

    KANEKO-ISHINO, Tomoko; ISHINO, Fumitoshi

    2015-01-01

    Mammals, including human beings, have evolved a unique viviparous reproductive system and a highly developed central nervous system. How did these unique characteristics emerge in mammalian evolution, and what kinds of changes did occur in the mammalian genomes as evolution proceeded? A key conceptual term in approaching these issues is “mammalian-specific genomic functions”, a concept covering both mammalian-specific epigenetics and genetics. Genomic imprinting and LTR retrotransposon-derived genes are reviewed as the representative, mammalian-specific genomic functions that are essential not only for the current mammalian developmental system, but also mammalian evolution itself. First, the essential roles of genomic imprinting in mammalian development, especially related to viviparous reproduction via placental function, as well as the emergence of genomic imprinting in mammalian evolution, are discussed. Second, we introduce the novel concept of “mammalian-specific traits generated by mammalian-specific genes from LTR retrotransposons”, based on the finding that LTR retrotransposons served as a critical driving force in the mammalian evolution via generating mammalian-specific genes. PMID:26666304

  19. Genomic Change, Retrotransposon Mobilization and Extensive Cytosine Methylation Alteration in Brassica napus Introgressions from Two Intertribal Hybridizations

    PubMed Central

    Zhang, Xueli; Ge, Xianhong; Shao, Yujiao; Sun, Genlou; Li, Zaiyun

    2013-01-01

    Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4–39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed. PMID:23468861

  20. Variation in Copy Number of Ty3/Gypsy Centromeric Retrotransposons in the Genomes of Thinopyrum intermedium and Its Diploid Progenitors

    PubMed Central

    Divashuk, Mikhail G.; Khuat, Thi Mai L.; Kroupin, Pavel Yu.; Kirov, Ilya V.; Romanov, Dmitry V.; Kiseleva, Anna V.; Khrustaleva, Ludmila I.; Alexeev, Dmitry G.; Zelenin, Alexandr S.; Klimushina, Marina V.; Razumova, Olga V.; Karlov, Gennady I.

    2016-01-01

    Speciation and allopolyploidization in cereals may be accompanied by dramatic changes in abundance of centromeric repeated transposable elements. Here we demonstrate that the reverse transcriptase part of Ty3/gypsy centromeric retrotransposon (RT-CR) is highly conservative in the segmental hexaploid Thinopyrum intermedium (JrJvsSt) and its possible diploid progenitors Th. bessarabicum (Jb), Pseudoroegneria spicata (St) and Dasypyrum villosum (V) but the abundance of the repeats varied to a large extent. Fluorescence in situ hybridization (FISH) showed hybridization signals in centromeric region of all chromosomes in the studied species, although the intensity of the signals drastically differed. In Th. intermedium, the strongest signal of RT-CR probe was detected on the chromosomes of Jv, intermediate on Jr and faint on Js and St subgenome suggesting different abundance of RT-CR on the individual chromosomes rather than the sequence specificity of RT-CRs of the subgenomes. RT-CR quantification using real-time PCR revealed that its content per genome in Th. bessarabicum is ~ 2 times and P. spicata is ~ 1,5 times higher than in genome of D. villosum. The possible burst of Ty3/gypsy centromeric retrotransposon in Th. intermedium during allopolyploidization and its role in proper mitotic and meiotic chromosome behavior in a nascent allopolyploid is discussed. PMID:27119343

  1. Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome.

    PubMed

    Coates, Brad S; Fraser, Lisa M; French, B Wade; Sappington, Thomas W

    2014-01-25

    The proliferation of retrotransposons within a genome can contribute to increased size and affect the function of eukaryotic genes. BEL/Pao-like long-terminal repeat (LTR) retrotransposons were annotated from the highly adaptable insect species Diabrotica virgifera virgifera, the Western corn rootworm, using survey sequences from bacterial artificial chromosome (BAC) inserts and contigs derived from a low coverage next-generation genome sequence assembly. Eleven unique D. v. virgifera BEL elements were identified that contained full-length gag-pol coding sequences, whereas 88 different partial coding regions were characterized from partially assembled elements. Estimated genome copy number for full and partial BEL-like elements ranged from ~8 to 1582 among individual contigs using a normalized depth of coverage (DOC) among Illumina HiSeq reads (total genome copy number ~8821). BEL element copy number was correlated among different D. v. virgifera populations (R2=0.9846), but individual element numbers varied ≤ 1.68-fold and the total number varied by ~527 copies. These data indicate that BEL element proliferation likely contributed to a large genome size, and suggest that differences in copy number are a source of genetic variability among D. v. virgifera. PMID:24498652

  2. Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome.

    PubMed

    Coates, Brad S; Fraser, Lisa M; French, B Wade; Sappington, Thomas W

    2013-10-25

    The proliferation of retrotransposons within a genome can contribute to increased size and affect the function of eukaryotic genes. BEL/Pao-like long-terminal repeat (LTR) retrotransposons were annotated from the highly adaptable insect species Diabrotica virgifera virgifera, the western corn rootworm, using survey sequences from bacterial artificial chromosome (BAC) inserts and contigs derived from a low coverage next-generation genome sequence assembly. Eleven unique D. v. virgifera BEL elements were identified that contained full-length gag-pol coding sequences, whereas 88 different partial coding regions were characterized from partially assembled elements. Estimated genome copy number for full and partial BEL-like elements ranged from ~8 to 1,582 among individual contigs using a normalized depth of coverage (DOC) among Illumina HiSeq reads (total genome copy number ~8,821). BEL element copy number was correlated among different D. v. virgifera populations (R(2)=0.9846), but individual element numbers varied≤1.68-fold and the total number varied by ~527 copies. These data indicate that BEL element proliferation likely contributed to a large genome size, and suggest that differences in copy number are a source of genetic variability among D. v. virgifera. PMID:24513336

  3. A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells

    PubMed Central

    Koziol, Uriel; Radio, Santiago; Smircich, Pablo; Zarowiecki, Magdalena; Fernández, Cecilia; Brehm, Klaus

    2015-01-01

    Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes. PMID:26133390

  4. A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3

    PubMed Central

    Chaurasiya, Kathy R.; Geertsema, Hylkje; Cristofari, Gaël; Darlix, Jean-Luc; Williams, Mark C.

    2012-01-01

    Reverse transcription in retroviruses and retrotransposons requires nucleic acid chaperones, which drive the rearrangement of nucleic acid conformation. The nucleic acid chaperone properties of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein have been extensively studied, and nucleic acid aggregation, duplex destabilization and rapid binding kinetics have been identified as major components of its activity. However, the properties of other nucleic acid chaperone proteins, such as retrotransposon Ty3 NC, a likely ancestor of HIV-1 NC, are not well understood. In addition, it is unclear whether a single zinc finger is sufficient to optimize the properties characteristic of HIV-1 NC. We used single-molecule DNA stretching as a method for detailed characterization of Ty3 NC chaperone activity. We found that wild type Ty3 NC aggregates single- and double-stranded DNA, weakly stabilizes dsDNA, and exhibits rapid binding kinetics. Single-molecule studies in the presence of Ty3 NC mutants show that the N-terminal basic residues and the unique zinc finger at the C-terminus are required for optimum chaperone activity in this system. While the single zinc finger is capable of optimizing Ty3 NC's DNA interaction kinetics, two zinc fingers may be necessary in order to facilitate the DNA destabilization exhibited by HIV-1 NC. PMID:21917850

  5. A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

    PubMed

    Chaurasiya, Kathy R; Geertsema, Hylkje; Cristofari, Gaël; Darlix, Jean-Luc; Williams, Mark C

    2012-01-01

    Reverse transcription in retroviruses and retrotransposons requires nucleic acid chaperones, which drive the rearrangement of nucleic acid conformation. The nucleic acid chaperone properties of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein have been extensively studied, and nucleic acid aggregation, duplex destabilization and rapid binding kinetics have been identified as major components of its activity. However, the properties of other nucleic acid chaperone proteins, such as retrotransposon Ty3 NC, a likely ancestor of HIV-1 NC, are not well understood. In addition, it is unclear whether a single zinc finger is sufficient to optimize the properties characteristic of HIV-1 NC. We used single-molecule DNA stretching as a method for detailed characterization of Ty3 NC chaperone activity. We found that wild type Ty3 NC aggregates single- and double-stranded DNA, weakly stabilizes dsDNA, and exhibits rapid binding kinetics. Single-molecule studies in the presence of Ty3 NC mutants show that the N-terminal basic residues and the unique zinc finger at the C-terminus are required for optimum chaperone activity in this system. While the single zinc finger is capable of optimizing Ty3 NC's DNA interaction kinetics, two zinc fingers may be necessary in order to facilitate the DNA destabilization exhibited by HIV-1 NC. PMID:21917850

  6. HSP90α plays an important role in piRNA biogenesis and retrotransposon repression in mouse

    PubMed Central

    Ichiyanagi, Tomoko; Ichiyanagi, Kenji; Ogawa, Ayako; Kuramochi-Miyagawa, Satomi; Nakano, Toru; Chuma, Shinichiro; Sasaki, Hiroyuki; Udono, Heiichiro

    2014-01-01

    HSP90, found in all kingdoms of life, is a major chaperone protein regulating many client proteins. We demonstrated that HSP90α, one of two paralogs duplicated in vertebrates, plays an important role in the biogenesis of fetal PIWI-interacting RNAs (piRNA), which act against the transposon activities, in mouse male germ cells. The knockout mutation of Hsp90α resulted in a large reduction in the expression of primary and secondary piRNAs and mislocalization of MIWI2, a PIWI homolog. Whereas the mutation in Fkbp6 encoding a co-chaperone reduced piRNAs of 28–32 nucleotides in length, the Hsp90α mutation reduced piRNAs of 24–32 nucleotides, suggesting the presence of both FKBP6-dependent and -independent actions of HSP90α. Although DNA methylation and mRNA levels of L1 retrotransposon were largely unchanged in the Hsp90α mutant testes, the L1-encoded protein was increased, suggesting the presence of post-transcriptional regulation. This study revealed the specialized function of the HSP90α isofom in the piRNA biogenesis and repression of retrotransposons during the development of male germ cells in mammals. PMID:25262350

  7. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1.

    PubMed

    Leung, Danny; Du, Tingting; Wagner, Ulrich; Xie, Wei; Lee, Ah Young; Goyal, Preeti; Li, Yujing; Szulwach, Keith E; Jin, Peng; Lorincz, Matthew C; Ren, Bing

    2014-05-01

    During mammalian development, DNA methylation patterns need to be reset in primordial germ cells (PGCs) and preimplantation embryos. However, many LTR retrotransposons and imprinted genes are impervious to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that a subset of such genomic regions are resistant to widespread erasure of DNA methylation in mouse embryonic stem cells (mESCs) lacking the de novo DNA methyltransferases (Dnmts) Dnmt3a and Dnmt3b. Intriguingly, these loci are enriched for H3K9me3 in mESCs, implicating this mark in DNA methylation homeostasis. Indeed, deletion of the H3K9 methyltransferase SET domain bifurcated 1 (Setdb1) results in reduced H3K9me3 and DNA methylation levels at specific loci, concomitant with increased 5-hydroxymethylation (5hmC) and ten-eleven translocation 1 binding. Taken together, these data reveal that Setdb1 promotes the persistence of DNA methylation in mESCs, likely reflecting one mechanism by which DNA methylation is maintained at LTR retrotransposons and imprinted genes during developmental stages when DNA methylation is reprogrammed. PMID:24757056

  8. NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans.

    PubMed Central

    Malik, H S; Eickbush, T H

    2000-01-01

    Phylogenetic analyses of non-LTR retrotransposons suggest that all elements can be divided into 11 lineages. The 3 oldest lineages show target site specificity for unique locations in the genome and encode an endonuclease with an active site similar to certain restriction enzymes. The more "modern" non-LTR lineages possess an apurinic endonuclease-like domain and generally lack site specificity. The genome sequence of Caenorhabditis elegans reveals the presence of a non-LTR retrotransposon that resembles the older elements, in that it contains a single open reading frame with a carboxyl-terminal restriction-like endonuclease domain. Located near the N-terminal end of the ORF is a cysteine protease domain not found in any other non-LTR element. The N2 strain of C. elegans appears to contain only one full-length and several 5' truncated copies of this element. The elements specifically insert in the Spliced leader-1 genes; hence the element has been named NeSL-1 (Nematode Spliced Leader-1). Phylogenetic analysis confirms that NeSL-1 branches very early in the non-LTR lineage and that it represents a 12th lineage of non-LTR elements. The target specificity of NeSL-1 for the spliced leader exons and the similarity of its structure to that of R2 elements leads to a simple model for its expression and retrotransposition. PMID:10628980

  9. Cognitive Function Related to the Sirh11/Zcchc16 Gene Acquired from an LTR Retrotransposon in Eutherians.

    PubMed

    Irie, Masahito; Yoshikawa, Masanobu; Ono, Ryuichi; Iwafune, Hirotaka; Furuse, Tamio; Yamada, Ikuko; Wakana, Shigeharu; Yamashita, Yui; Abe, Takaya; Ishino, Fumitoshi; Kaneko-Ishino, Tomoko

    2015-09-01

    Gene targeting of mouse Sushi-ichi-related retrotransposon homologue 11/Zinc finger CCHC domain-containing 16 (Sirh11/Zcchc16) causes abnormal behaviors related to cognition, including attention, impulsivity and working memory. Sirh11/Zcchc16 encodes a CCHC type of zinc-finger protein that exhibits high homology to an LTR retrotransposon Gag protein. Upon microdialysis analysis of the prefrontal cortex region, the recovery rate of noradrenaline (NA) was reduced compared with dopamine (DA) after perfusion of high potassium-containing artificial cerebrospinal fluid in knockout (KO) mice. These data indicate that Sirh11/Zcchc16 is involved in cognitive function in the brain, possibly via the noradrenergic system, in the contemporary mouse developmental systems. Interestingly, it is highly conserved in three out of the four major groups of the eutherians, euarchontoglires, laurasiatheria and afrotheria, but is heavily mutated in xenarthran species such as the sloth and armadillo, suggesting that it has contributed to brain evolution in the three major eutherian lineages, including humans and mice. Sirh11/Zcchc16 is the first SIRH gene to be involved in brain function, instead of just the placenta, as seen in the case of Peg10, Peg11/Rtl1 and Sirh7/Ldoc1. PMID:26402067

  10. Protein Interactions Involved in tRNA Gene-Specific Integration of Dictyostelium discoideum Non-Long Terminal Repeat Retrotransposon TRE5-A▿

    PubMed Central

    Chung, Thanh; Siol, Oliver; Dingermann, Theodor; Winckler, Thomas

    2007-01-01

    Mobile genetic elements that reside in gene-dense genomes face the problem of avoiding devastating insertional mutagenesis of genes in their host cell genomes. To meet this challenge, some Saccharomyces cerevisiae long terminal repeat (LTR) retrotransposons have evolved targeted integration at safe sites in the immediate vicinity of tRNA genes. Integration of yeast Ty3 is mediated by interactions of retrotransposon protein with the tRNA gene-specific transcription factor IIIB (TFIIIB). In the genome of the social amoeba Dictyostelium discoideum, the non-LTR retrotransposon TRE5-A integrates ∼48 bp upstream of tRNA genes, yet little is known about how the retrotransposon identifies integration sites. Here, we show direct protein interactions of the TRE5-A ORF1 protein with subunits of TFIIIB, suggesting that ORF1p is a component of the TRE5-A preintegration complex that determines integration sites. Our results demonstrate that evolution has put forth similar solutions to prevent damage of diverse, compact genomes by different classes of mobile elements. PMID:17923679

  11. A new member of a family of site-specific retrotransposons is present in the spliced leader RNA genes of Trypanosoma cruzi.

    PubMed Central

    Villanueva, M S; Williams, S P; Beard, C B; Richards, F F; Aksoy, S

    1991-01-01

    A new member of a family of site-specific retrotransposons is described in the New World trypanosome Trypanosoma cruzi. This element, CZAR (cruzi-associated retrotransposon), resembles two previously described retrotransposons found in the African trypanosome T. brucei gambiense and the mosquito trypanosomatid Crithidia fasciculata in specifically inserting between nucleotides 11 and 12 of the highly conserved 39-mer of the spliced leader RNA (SL-RNA) gene. CZAR is similar in overall organization to the other two SL-RNA-associated elements. It possesses two potential long open reading frames which resemble the gag and pol genes of retroviruses. In the pol open reading frame, all three elements contain similarly arranged endonuclease domains and share extensive amino acid homology in the reverse transcriptase region. All are associated with the SL-RNA gene locus and are present in low copy numbers. They do not appear to have 5' truncated versions. All three retrotransposons are otherwise quite distinct from one another, with no significant overall amino acid homology. The presence of such retroelements inserted into the identical site within SL-RNA gene sequences in at least three evolutionarily distant trypanosomatid species argues for a functional role. Because these elements appear to have a precise target site requirement for integration, we refer to them as SL siteposons. Images PMID:1719380

  12. The Juan non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity

    PubMed Central

    Biedler, James K; Tu, Zhijian

    2007-01-01

    Background In contrast to DNA-mediated transposable elements (TEs), retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs), are generally considered to have a much lower propensity towards horizontal transfer. Detailed studies on site-specific non-LTR families have demonstrated strict vertical transmission. More studies are needed with non-site-specific non-LTR families to determine whether strict vertical transmission is a phenomenon related to site specificity or a more general characteristic of all non-LTRs. Juan is a Jockey clade non-LTR retrotransposon first discovered in mosquitoes that is widely distributed in the mosquito family Culicidae. Being a non-site specific non-LTR, Juan offers an opportunity to further investigate the hypothesis that non-LTRs are genomic elements that are primarily vertically transmitted. Results Systematic analysis of the ~1.3 Gbp Aedes aegypti (Ae. aegypti) genome sequence suggests that Juan-A is the only Juan-type non-LTR in Aedes aegypti. Juan-A is highly reiterated and comprises approximately 3% of the genome. Using minimum cutoffs of 90% length and 70% nucleotide (nt) identity, 663 copies were found by BLAST using the published Juan-A sequence as the query. All 663 copies are at least 95% identical to Juan-A, while 378 of these copies are 99% identical to Juan-A, indicating that the Juan-A family has been transposing recently in evolutionary history. Using the 0.34 Kb 5' UTR as the query, over 2000 copies were identified that may contain internal promoters, leading to questions on the genomic impact of Juan-A. Juan sequences were obtained by PCR, library screening, and database searches for 18 mosquito species of six genera including Aedes, Ochlerotatus, Psorophora, Culex, Deinocerites, and Wyeomyia. Comparison of host and Juan phylogenies shows overall congruence with few exceptions. Conclusion Juan-A is a major genomic component in Ae. aegypti and it has been retrotransposing recently in

  13. Identification of a 5' truncated non-LTR-retrotransposon, YAKPs1, from the variegated cutworm, Peridroma saucia, using PCR.

    PubMed

    Ring, M; Pfeifer, T A; Grigliatti, T A

    1996-05-01

    Retrotransposable elements encode for several polypeptides that contain a number of conserved amino acid motifs, especially in the region encoding reverse transcriptase. We have used these motifs to design primers for the PCR amplification of retrotransposon DNA. These primers have allowed us to isolate a retroposon, or LINE (long interspersed nuclear element), from the pest insect, Peridroma saucia. DNA sequence analysis of this element, YAKPs1, demonstrated a high degree of homology to a number of retroposons from Drosophila melanogaster, in particular the Fw and Doc elements with homologies of up to 69%. Determination of the complete sequence of the YAKPs1 element will enable a detailed analysis of its evolutionary relatedness to other elements as well as a greater insight into its mode of action. PMID:8763168

  14. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates.

    PubMed

    Naville, M; Warren, I A; Haftek-Terreau, Z; Chalopin, D; Brunet, F; Levin, P; Galiana, D; Volff, J-N

    2016-04-01

    Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage. PMID:26899828

  15. An Evaluation of a SVA Retrotransposon in the FUS Promoter as a Transcriptional Regulator and Its Association to ALS

    PubMed Central

    Khursheed, Kejhal; Shatunov, Aleksey; Morrison, Karen E.; Shaw, Pamela J.; Shaw, Christopher E.; Smith, Bradley; Breen, Gerome; Al-Chalabi, Ammar; Moss, Diana; Bubb, Vivien J.; Quinn, John P.

    2014-01-01

    Genetic mutations of FUS have been linked to many diseases including Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration. A primate specific and polymorphic retrotransposon of the SINE-VNTR-Alu (SVA) family is present upstream of the FUS gene. Here we have demonstrated that this retrotransposon can act as a classical transcriptional regulatory domain in the context of a reporter gene construct both in vitro in the human SK-N-AS neuroblastoma cell line and in vivo in a chick embryo model. We have also demonstrated that the SVA is composed of multiple distinct regulatory domains, one of which is a variable number tandem repeat (VNTR). The ability of the SVA and its component parts to direct reporter gene expression supported a hypothesis that this region could direct differential FUS expression in vivo. The SVA may therefore contribute to the modulation of FUS expression exhibited in and associated with neurological disorders including ALS where FUS regulation may be an important parameter in progression of the disease. As VNTRs are often clinical associates for disease progression we determined the extent of polymorphism within the SVA. In total 2 variants of the SVA were identified based within a central VNTR. Preliminary analysis addressed the association of these SVA variants within a small sporadic ALS cohort but did not reach statistical significance, although we did not include other parameters such as SNPs within the SVA or an environmental factor in this analysis. The latter may be particularly important as the transcriptional and epigenetic properties of the SVA are likely to be directed by the environment of the cell. PMID:24608899

  16. Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae)

    PubMed Central

    Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

    2013-01-01

    Background and Aims The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. Methods A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100–500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Key Results Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S–5·8S–25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. Conclusions The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species. PMID:23666888

  17. Nimbus (BgI): An active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata✰

    PubMed Central

    Raghavan, Nithya; Tettelin, Hervé; Miller, André; Hostetler, Jessica; Tallon, Luke; Knight, Matty

    2009-01-01

    The freshwater snail Biomphalaria glabrata is closely associated with the transmission of human schistosomiasis. An ecologically sound method has been proposed to control schistosomiasis using genetically modified snails to displace endemic, susceptible ones. To assess the viability of this form of biological control, studies towards understanding the molecular makeup of the snail relative to the presence of endogenous mobile genetic elements are being undertaken since they can be exploited for genetic transformation studies. We previously cloned a 1.95 Kb BamHI fragment in B. glabrata (BGR2) with sequence similarity to the human long interspersed nuclear element (LINE or L1). A contiguous, full-length sequence corresponding to BGR2, hereafter-named nimbus (BgI), has been identified from a B. glabrata bacterial artificial chromosome (BAC) library. Sequence analysis of the 65,764 bp BAC insert contained one full-length, complete nimbus (BgI) element (element I), two full-length elements (elements II and III) containing deletions and flanked by target site duplications and 10 truncated copies. The intact nimbus (BgI) contained two open reading frames (ORFs 1 and 2) encoding the characteristic hallmark domains found in non-long terminal repeat retrotransposons belonging to the I clade; a nucleic acid binding protein in ORF1 and an apurinic/apyrimidinic endonuclease, reverse transcriptase and RNase H in ORF2. Phylogenetic analysis revealed that nimbus (BgI) is closely related to Drosophila (I factor), mosquito Aedes aegypti (MosquI) and chordate ascidian Ciona intestinalis (CiI) retrotransposons. Nimbus (BgI) represents the first complete mobile element characterized from a mollusk that appears to be transcriptionally active and is widely distributed in snails of the neotropics and the Old World. PMID:17521654

  18. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines

    PubMed Central

    Sciamanna, Ilaria; Gualtieri, Alberto; Cossetti, Cristina; Osimo, Emanuele Felice; Ferracin, Manuela; Macchia, Gianfranco; Aricò, Eleonora; Prosseda, Gianni; Vitullo, Patrizia; Misteli, Tom; Spadafora, Corrado

    2013-01-01

    LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the

  19. Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications

    PubMed Central

    2013-01-01

    Background Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments. The nature of divergences between co-occurring sympatric species, factors contributing to reproductive isolation and modes of genome evolution is a much debated topic in evolutionary biology addressed by various experimental tools. To the best of our knowledge, nobody approached this field using molecular cytogenetics. We examined chromosomes and genomes of one postglacial species pair, sympatric European winter-spawning Coregonus albula and the local endemic dwarf-sized spring-spawning C. fontanae, both originating in Lake Stechlin. We have employed molecular cytogenetic tools to identify the genomic differences between the two species of the sympatric pair on the sub-chromosomal level of resolution. Results Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C. albula and C. fontanae genomes. In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8–10 chromosomes possessed these genes. To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. The amplified retrotransposon Rex1 was used as a probe for FISH mapping onto chromosomes of both species. These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species. Conclusion We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis. We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates

  20. A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5' truncations

    PubMed Central

    2010-01-01

    Background Rotifers of the class Bdelloidea are microscopic freshwater invertebrates best known for: their capacity for anhydrobiosis; the lack of males and meiosis; and for the ability to capture genes from other non-metazoan species. Although genetic exchange between these animals might take place by non-canonical means, the overall lack of meiosis and syngamy should greatly impair the ability of transposable elements (TEs) to spread in bdelloid populations. Previous studies demonstrated that bdelloid chromosome ends, in contrast to gene-rich regions, harbour various kinds of TEs, including specialized telomere-associated retroelements, as well as DNA TEs and retrovirus-like retrotransposons which are prone to horizontal transmission. Vertically-transmitted retrotransposons have not previously been reported in bdelloids and their identification and studies of the patterns of their distribution and evolution could help in the understanding of the high degree of TE compartmentalization within bdelloid genomes. Results We identified and characterized a non-long terminal repeat (LTR) retrotransposon residing primarily in subtelomeric regions of the genome in the bdelloid rotifer Adineta vaga. Contrary to the currently prevailing views on the mode of proliferation of non-LTR retrotransposons, which results in frequent formation of 5'-truncated ('dead-on-arrival') copies due to the premature disengagement of the element-encoded reverse transcriptase from its template, this non-LTR element, Hebe, is represented only by non-5'-truncated copies. Most of these copies, however, were subject to internal deletions associated with microhomologies, a hallmark of non-homologous end-joining events. Conclusions The non-LTR retrotransposon Hebe from the bdelloid rotifer A. vaga was found to undergo frequent microhomology-associated deletions, rather than 5'-terminal truncations characteristic of this class of retrotransposons, and to exhibit preference for telomeric localization

  1. Chicken repeat 1 elements contain a pol-like open reading frame and belong to the non-long terminal repeat class of retrotransposons.

    PubMed Central

    Burch, J B; Davis, D L; Haas, N B

    1993-01-01

    Chicken genomes contain approximately 30,000 chicken repeat 1 (CR1) elements scattered among single-copy sequences, but no information has yet been presented to account for how these elements could have dispersed. The fact that CR1 elements have common (although atypical) 3' ends and variable 5' truncations suggested to us that they might belong to the class of non-long terminal repeat retrotransposons that encode reverse transcriptases. From an analysis of unusually large CR1 elements, we now provide evidence for the presence of such a reverse transcriptase open reading frame. CR1 elements are distantly related to previously described non-long terminal repeat retrotransposons; however, we find that frog and torpedo ray genomes contain dispersed open reading frame segments that have > 50% identity to the CR1 open reading frame. This result suggests that CR1-like elements exist in several vertebrate classes that have evolved independently for approximately 400 million years. PMID:8396264

  2. Identification of a novel PNMA-MS1 gene in marsupials suggests the LTR retrotransposon-derived PNMA genes evolved differently in marsupials and eutherians.

    PubMed

    Iwasaki, Sawa; Suzuki, Shunsuke; Pelekanos, Matthew; Clark, Helen; Ono, Ryuichi; Shaw, Geoff; Renfree, Marilyn B; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2013-10-01

    Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians. PMID:23704700

  3. Differential Expression of Retrotransposon WIS 2-1A Response to Vacuum, Low-Energy N+ Implantation and 60Coγ-ray Irradiation in Wheat

    NASA Astrophysics Data System (ADS)

    Zhao, Huiru; Gu, Yunhong; Ya, Huiyuan; Jiao, Zhen; Qin, Guangyong

    2009-02-01

    Mutagenesis and retrotransposons have a close relationship, but little attention has been paid yet to the activity of retrotransposons produced by physical mutagens. The variation of retrotransposon WIS 2-1A activity in wheat (Triticum aestivum L.) embryos at three different growth times (30 h, 45 h and 60 h) was investigated after they had been treated with N+ implantation in a vacuum of 5 × 10-2 Pa and irradiation by 60Coγ-ray respectively. For each of the three growth times the expression of WIS 2-1A showed almost entirely a same trend of downregulation, upregulation, then downregulation, and upregulation again with the increase in dose of N+ implantation, but the expression appeared irregular with the increase in irradiation of 60Coγ-ray. In conclusion, the acutely activating effect of WIS 2-1A stimulated by vacuum and high dose N+ implantation within a shorter incubation time may provide a convenient tool to advance the research on mutagenic breeding and function genes.

  4. Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes.

    PubMed

    Conte, Caroline; Dastugue, Bernard; Vaury, Chantal

    2002-03-01

    We recently reported a novel transposition system in which two retroelements from Drosophila melanogaster, ZAM and Idefix, are highly mobilized and preferentially insert within intergenic regions. Among the loci where new copies are detected, a hot spot for their insertion was identified at the white locus, where up to three elements occurred within a 3-kb fragment upstream of the transcriptional start site of white. We have used these insertions as molecular entry points to throw light on the mutagenic effect exerted by multiple insertions of retrotransposons within intergenic regions of a genome. Analysis of the molecular mechanisms by which ZAM and Idefix elements interfere with the regulation of the white gene has shown that ZAM bears cis-acting regulatory sequences able to enhance transcription of the white gene in the eyes of the flies. This activation may be counteracted by Idefix, which acts as an insulator able to isolate the white gene from the upstream ZAM enhancer. In addition to revealing a novel insulator sequence with its own specific features, our data clearly illustrate how retroelements can act as epigenetic factors able to interfere with the transcriptional regulation of their host. PMID:11865056

  5. Retrotransposon-microsatellite amplified polymorphism, an electrophoretic approach for studying genetic variability among Schistosoma japonicum geographical isolates.

    PubMed

    Li, Juan; Zhao, Guang-Hui; Zhou, Dong-Hui; Sugiyama, Hiromu; Nisbet, Alasdair J; Li, Xiao-Yan; Zou, Feng-Cai; Li, Hai-Long; Ai, Lin; Zhu, Xing-Quan

    2012-09-01

    In the present study, retrotransposon-microsatellite amplified polymorphism (REMAP) was used to examine genetic variability among Schistosoma japonicum isolates from different endemic provinces in mainland China, using S. japonicum from Japan and the Philippines for comparison. Of the 50 primer combinations screened, eight produced highly reproducible REMAP fragments. Using these primers, 190 distinct DNA fragments were generated in total, of which 147 (77.37%) were polymorphic, indicating considerable genetic variation among the 43 S. japonicum isolates examined. The percentage of polymorphic bands (PPB) among S. japonicum isolates from mainland China, Japan, and the Philippines was 77.37%; PPB values of 18.42% and 53.68% were found among isolates from southwestern (SW) China and the lower Yangtze/Zhejiang province in eastern (E) China, respectively. Based on REMAP profiles, unweighted pair-group method with arithmetic averages (UPGMA) dendrogram analysis revealed that all of the S. japonicum samples grouped into three distinct clusters: parasites from mainland China, Japan, and the Philippines were clustered in each individual clade. Within the mainland China cluster, SW China isolates (from Sichuan and Yunnan provinces) grouped together, whereas worms from E China (Zhejiang, Anhui, Jiangxi, Jiangsu, Hunan, and Hubei provinces) grouped together. These results demonstrated that the REMAP marker system provides a reliable electrophoretic technique for studying genetic diversity and population structures of S. japonicum isolates from mainland China, and could be applied to other pathogens of human and animal health significance. PMID:23019103

  6. Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers

    PubMed Central

    Renaut, Sebastien; Rowe, Heather C.; Ungerer, Mark C.; Rieseberg, Loren H.

    2014-01-01

    Hybridization is thought to play an important role in plant evolution by introducing novel genetic combinations and promoting genome restructuring. However, surprisingly little is known about the impact of hybridization on transposable element (TE) proliferation and the genomic response to TE activity. In this paper, we first review the mechanisms by which homoploid hybrid species may arise in nature. We then present hybrid sunflowers as a case study to examine transcriptional activity of long terminal repeat retrotransposons in the annual sunflowers Helianthus annuus, Helianthus petiolaris and their homoploid hybrid derivatives (H. paradoxus, H. anomalus and H. deserticola) using high-throughput transcriptome sequencing technologies (RNAseq). Sampling homoploid hybrid sunflower taxa revealed abundant variation in TE transcript accumulation. In addition, genetic diversity for several candidate genes hypothesized to regulate TE activity was characterized. Specifically, we highlight one candidate chromatin remodelling factor gene with a direct role in repressing TE activity in a hybrid species. This paper shows that TE amplification in hybrid lineages is more idiosyncratic than previously believed and provides a first step towards identifying the mechanisms responsible for regulating and repressing TE expansions. PMID:24958919

  7. Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene

    PubMed Central

    Saenko, Suzanne V.; Lamichhaney, Sangeet; Barrio, Alvaro Martinez; Rafati, Nima; Andersson, Leif; Milinkovitch, Michel C.

    2015-01-01

    The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes, transcriptomic and genomic next-generation sequencing, exome assembly, and genotyping of SNPs in multiple families, we delimit the genomic interval bearing the causal mutation of amelanism, the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval, we identify that the insertion of an LTR-retrotransposon in its 11th intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white, instead of black, borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches, our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish, this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages. PMID:26597053

  8. Argonaute Proteins Affect siRNA Levels and Accumulation of a Novel Extrachromosomal DNA from the Dictyostelium Retrotransposon DIRS-1*

    PubMed Central

    Boesler, Benjamin; Meier, Doreen; Förstner, Konrad U.; Friedrich, Michael; Hammann, Christian; Sharma, Cynthia M.; Nellen, Wolfgang

    2014-01-01

    The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms. We investigated the role of two of the five Argonaute proteins of D. discoideum, AgnA and AgnB, in DIRS-1 silencing. Deletion of agnA resulted in the accumulation of DIRS-1 transcripts, the expression of DIRS-1-encoded proteins, and the loss of most DIRS-1-derived secondary siRNAs. Simultaneously, extrachromosomal single-stranded DIRS-1 DNA accumulated in the cytoplasm of agnA− strains. These DNA molecules appear to be products of reverse transcription and thus could represent intermediate structures before transposition. We further show that transitivity of endogenous siRNAs is impaired in agnA− strains. The deletion of agnB alone had no strong effect on DIRS-1 transposon regulation. However, in agnA−/agnB− double mutant strains strongly reduced accumulation of extrachromosomal DNA compared with the single agnA− strains was observed. PMID:25352599

  9. Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer

    PubMed Central

    Stacey, Simon N.; Kehr, Birte; Gudmundsson, Julius; Zink, Florian; Jonasdottir, Aslaug; Gudjonsson, Sigurjon A.; Sigurdsson, Asgeir; Halldorsson, Bjarni V.; Agnarsson, Bjarni A.; Benediktsdottir, Kristrun R.; Aben, Katja K.H.; Vermeulen, Sita H.; Cremers, Ruben G.; Panadero, Angeles; Helfand, Brian T.; Cooper, Phillip R.; Donovan, Jenny L.; Hamdy, Freddie C.; Jinga, Viorel; Okamoto, Ichiro; Jonasson, Jon G.; Tryggvadottir, Laufey; Johannsdottir, Hrefna; Kristinsdottir, Anna M.; Masson, Gisli; Magnusson, Olafur T.; Iordache, Paul D.; Helgason, Agnar; Helgason, Hannes; Sulem, Patrick; Gudbjartsson, Daniel F.; Kong, Augustine; Jonsson, Eirikur; Barkardottir, Rosa B.; Einarsson, Gudmundur V.; Rafnar, Thorunn; Thorsteinsdottir, Unnur; Mates, Ioan N.; Neal, David E.; Catalona, William J.; Mayordomo, José I.; Kiemeney, Lambertus A.; Thorleifsson, Gudmar; Stefansson, Kari

    2016-01-01

    Transcriptional and splicing anomalies have been observed in intron 8 of the CASP8 gene (encoding procaspase-8) in association with cutaneous basal-cell carcinoma (BCC) and linked to a germline SNP rs700635. Here, we show that the rs700635[C] allele, which is associated with increased risk of BCC and breast cancer, is protective against prostate cancer [odds ratio (OR) = 0.91, P = 1.0 × 10−6]. rs700635[C] is also associated with failures to correctly splice out CASP8 intron 8 in breast and prostate tumours and in corresponding normal tissues. Investigation of rs700635[C] carriers revealed that they have a human-specific short interspersed element-variable number of tandem repeat-Alu (SINE-VNTR-Alu), subfamily-E retrotransposon (SVA-E) inserted into CASP8 intron 8. The SVA-E shows evidence of prior activity, because it has transduced some CASP8 sequences during subsequent retrotransposition events. Whole-genome sequence (WGS) data were used to tag the SVA-E with a surrogate SNP rs1035142[T] (r2 = 0.999), which showed associations with both the splicing anomalies (P = 6.5 × 10−32) and with protection against prostate cancer (OR = 0.91, P = 3.8 × 10−7). PMID:26740556

  10. Cognitive Function Related to the Sirh11/Zcchc16 Gene Acquired from an LTR Retrotransposon in Eutherians

    PubMed Central

    Irie, Masahito; Yoshikawa, Masanobu; Ono, Ryuichi; Iwafune, Hirotaka; Furuse, Tamio; Yamada, Ikuko; Wakana, Shigeharu; Yamashita, Yui; Abe, Takaya; Ishino, Fumitoshi; Kaneko-Ishino, Tomoko

    2015-01-01

    Gene targeting of mouse S ushi- i chi-related r etrotransposon h omologue 11 / Z inc finger CCHC domain-containing 16 (Sirh11/Zcchc16) causes abnormal behaviors related to cognition, including attention, impulsivity and working memory. Sirh11/Zcchc16 encodes a CCHC type of zinc-finger protein that exhibits high homology to an LTR retrotransposon Gag protein. Upon microdialysis analysis of the prefrontal cortex region, the recovery rate of noradrenaline (NA) was reduced compared with dopamine (DA) after perfusion of high potassium-containing artificial cerebrospinal fluid in knockout (KO) mice. These data indicate that Sirh11/Zcchc16 is involved in cognitive function in the brain, possibly via the noradrenergic system, in the contemporary mouse developmental systems. Interestingly, it is highly conserved in three out of the four major groups of the eutherians, euarchontoglires, laurasiatheria and afrotheria, but is heavily mutated in xenarthran species such as the sloth and armadillo, suggesting that it has contributed to brain evolution in the three major eutherian lineages, including humans and mice. Sirh11/Zcchc16 is the first SIRH gene to be involved in brain function, instead of just the placenta, as seen in the case of Peg10, Peg11/Rtl1 and Sirh7/Ldoc1. PMID:26402067